Stress-regulated genes of plants, transgenic plants containing same, and methods of use

ABSTRACT

Clusters of plant genes that are regulated in response to one or more stress conditions are provided, as are isolated plant stress-regulated genes, including portions thereof comprising a coding sequence or a regulatory element, and to consensus sequences comprising a plant stress-regulated regulatory element. In addition, a recombinant polynucleotide, which includes a plant stress-regulated gene, or functional portion thereof, operatively linked to a heterologous nucleotide sequence, is provided, as are transgenic plants, which contain a plant stress-regulated gene or functional portion thereof that was introduced into a progenitor cell of the plant. Also provided are methods of using a plant stress-regulated gene to confer upon a plant a selective advantage to a stress condition, methods of identifying an agent that modulates the activity of a plant stress-regulated regulatory element, and methods of determining whether a plant has been exposed to a stress.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application Ser. No. 11/299,286 (filed Dec. 9, 2005; pending), which is a continuation of application Ser. No. 09/938,842 (filed Aug. 24, 2001; now U.S. Pat. No. 7,109,033), which claims the benefit under 35 U.S.C. 119(e) of U.S. Ser. No. 60/227,866, filed Aug. 24, 2000; U.S. Ser. No. 60/264,647, filed Jan. 26, 2001; and U.S. Ser. No. 60/300,111, filed Jun. 22, 2001. Disclosures of the foregoing applications are hereby incorporated by reference herein in their entirety and for all purposes.

Three CD-R compact discs, labeled “Copy 1”, “Copy 2”, and “CRF” and having the files listed below, are submitted in parent application Ser. No. 09/938,842 (filed Aug. 24, 2001; now U.S. Pat. No. 7,109,033) and are incorporated herein by reference. Copy 1 and Copy 2 each contain two text documents: 1) a file named SCRIP1300-3_SEQUENCE_LISTING, which contains the Sequence Listing, was created on Dec. 21, 2001 (and recorded on the CD-R on Dec. 21, 2001), and is 9,972 KB in size; and 2) a file named SCRIP1300-3_Table_(—)32, which contains Table 32, was created on Aug. 20, 2001 (and recorded on the CD-R on Aug. 21, 2001), and is 1,251 KB in size. The CRF contains a single file named SCRIP1300-3_SEQUENCE_LISTING, which contains the Sequence Listing, was created on Dec. 21, 2001 (and recorded on the CD-R on Dec. 21, 2001), is 9,972 KB in size, and is identical to the files having the same name on Copy 1 and Copy 2.

FIELD OF THE INVENTION

The present invention relates generally to plant genes, the expression of which are regulated in response to stress, and more specifically to the gene regulatory elements involved in a stress-induced response in plants, to uses of the coding sequences and regulatory elements of such plant stress-regulated genes, and to transgenic plants genetically modified to express such a coding sequence or to express a heterologous polynucleotide from such a regulatory element.

BACKGROUND INFORMATION

Microarray technology is a powerful tool that can be used to identify the presence and level of expression of a large number of polynucleotides in a single assay. A microarray is formed by linking a large number of discrete polynucleotide sequences, for example, a population of polynucleotides representative of a genome of an organism, to a solid support such as a microchip, glass slide, or the like, in a defined pattern. By contacting the microarray with a nucleic acid sample obtained from a cell of interest, and detecting those polynucleotides expressed in the cell can hybridize specifically to complementary sequences on the chip, the pattern formed by the hybridizing polynucleotides allows the identification of clusters of genes that are expressed in the cell. Furthermore, where each polynucleotide linked to the solid support is known, the identity of the hybridizing sequences from the nucleic acid sample can be identified.

A strength of microarray technology is that it allows the identification of differential gene expression simply by comparing patterns of hybridization. For example, by comparing the hybridization pattern of nucleic acid molecules obtained from cells of an individual suffering from a disease with the nucleic acids obtained from the corresponding cells of a healthy individual, genes that are differentially expressed can be identified. The identification of such differentially expressed genes provides a means to identify new genes, and can provide insight as to the etiology of a disease.

Microarray technology has been widely used to identify patterns of gene expression associated with particular stages of development or of disease conditions in animal model systems, and is being applied to the identification of specific patterns of gene expression in humans. The recent availability of information for the genomes of plants provides a means to adapt microarray technology to the study of plant gene expression.

Plants and plant products provide the primary sustenance, either directly or indirectly, for all animal life, including humans. For the majority of the world's human population and for many animals, plants and plant products provide the sole source of nutrition. As the world population increases, the best hope to prevent widespread famine is to increase the quantity and improve the quality of food crops, and to make the crops available to the regions of the world most in need of food.

Throughout history, a continual effort has been made to increase the yield and nutritious value of food crops. For centuries, plants having desirable characteristics such as greater resistance to drought conditions or increased size of fruit were crossbred and progeny plants exhibiting the desired characteristics were selected and used to produce seed or cuttings for propagation. Using such classical genetic methods, plants having, for example, greater disease resistance, increased yield, and better flavor have been obtained. The identification of plant genes involved in conferring a selective advantage on the plant to an environmental challenge would facilitate the generation and yield of plants, thereby increasing the available food supply to an increasing world population. The involvement of these genes in a single organism to responses to multiple stress conditions, however, remains unknown. Thus, a need exists to identify plant genes and polynucleotides that are involved in modulating the response of a plant to changing environmental conditions. The present invention satisfies this need and provides additional advantages.

SUMMARY OF THE INVENTION

The present invention relates to clusters of genes that are regulated in response to a stress condition in plants. Such clusters include, for example, plant polynucleotides whose expression is altered in response to two or more different stress conditions; and plant polynucleotides the expression of which are altered in response to one stress condition, but not to others. The identification of such clusters, using microarray technology, has allowed the identification of plant stress-regulated genes in Arabidopsis thaliana (see Tables 1 and 2); and homologs and orthologs thereof in other plant species (see Table 32). Thus, the invention provides isolated polynucleotide portions of Arabidopsis plant stress-regulated genes, and homologs and orthologs thereof; variants of such sequences, and polynucleotides encoding substantially similar plant stress-regulated polypeptides expressed therefrom. Such sequences include, for example, sequences encoding transcription factors; enzymes, including kinases; and structural proteins, including channel proteins (see Tables 29-31). Accordingly, the present invention also relates to an isolated polynucleotide comprising all or a portion of a plant stress-regulated gene, and to polynucleotide portions thereof, including a coding region (open reading frame), which encodes all or a portion of a stress-regulated polypeptide, for example, as set forth in SEQ ID NOS:1-2703; and a regulatory element involved in regulating the response of the plant to a stress condition such exposure to an abnormal level of salt, osmotic pressure, temperature or any combination thereof, for example, as set forth in SEQ ID NOS:2704-5379.

The present invention also relates to a recombinant polynucleotide, which contains a nucleotide sequence of a plant stress-regulated gene or functional portion thereof operatively linked to a heterologous nucleotide sequence. In one embodiment, the recombinant polynucleotide comprises a plant stress-regulated gene regulatory element operatively linked to a heterologous nucleotide sequence, which is not regulated by the regulatory element in a naturally occurring plant. The heterologous nucleotide sequence, when expressed from the regulatory element, can confer a desirable phenotype to a plant cell containing the recombinant polynucleotide. In another embodiment, the recombinant polynucleotide comprises a coding region, or portion thereof, of a plant stress-regulated gene operatively linked to a heterologous promoter. The heterologous promoter provides a means to express an encoded stress-regulated polypeptide constitutively, or in a tissue-specific or phase-specific manner.

Accordingly, in one aspect, the present invention provides an isolated polynucleotide comprising a nucleotide sequence of a plant gene that hybridizes under stringent conditions, preferably high stringency conditions, to any one of SEQ ID NOS:1-5379 (see Tables 1 and 2), including to a coding region (SEQ ID NOS:1-2703) or a regulatory region, which can alter transcription of an operatively linked nucleic acid sequence in response to an abiotic stress (SEQ ID NOS:2704-5379; see Table 2), or to a complement thereof. Additional aspects provide sequences that hybridize under stringent conditions, preferably high stringency conditions, to the complements of SEQ ID NO 1-1261 (cold responsive genes; Tables 3-6), SEQ ID NOS:2227-2427 (saline responsive genes; Tables 7-10), SEQ ID NOS:2428-2585 (osmotic responsive genes; Tables 11-14), SEQ ID NOS:1699-1969 (cold and osmotic responsive genes; Tables 15-17), SEQ ID NOS:1970-2226 (cold and saline responsive genes; Tables 18-20), SEQ ID NOS:2586-2703 (osmotic and saline responsive genes; Tables 21-23), and SEQ ID NOS:1262-1698 (cold, osmotic and saline responsive genes; Tables 24-26), and which can comprise regulatory regions that can alter transcription in response to cold stress, osmotic stress, saline stress, or combinations thereof (SEQ ID NOS:2704-5379; see Table 2). Also provided are nucleotide sequences complementary thereto, and expression cassettes, plants and seeds comprising any of the above isolated sequences.

In another aspect, the present invention provides an isolated polynucleotide comprising a plant nucleotide sequence that hybridizes under stringent conditions, preferably high stringency conditions, to the complement of any one of SEQ ID NOS:1-2703 (Table 1), including to a coding region thereof (SEQ ID NOS:2704-5379), wherein expression of said coding region is altered in response to an abiotic stress. Additional aspects provide sequences that hybridize under high stringency conditions to the complements of SEQ ID NO 1-1261 (cold responsive genes; Tables 3-6), SEQ ID NOS:2227-2427 (saline responsive genes; Tables 7-10), SEQ ID NOS:2428-2585 (osmotic responsive genes; Tables 11-14), SEQ ID NOS:1699-1969 (cold and osmotic responsive genes; Tables 15-17), SEQ ID NOS:1970-2226 (cold and saline responsive genes; Tables 18-20), SEQ ID NOS:2586-2703 (osmotic and saline responsive genes; Tables 21-23), and SEQ ID NOS:1262-1698 (cold, osmotic and saline responsive genes; Tables 24-26), and which can comprise a coding region whose transcription is altered in response to cold stress, osmotic stress, saline stress, or a combination thereof. Also provided are nucleotide sequences complementary thereto, and expression cassettes, plants and seeds comprising any of the above sequences.

The invention further relates to a method of producing a transgenic plant, which comprises at least one plant cell that exhibits altered responsiveness to a stress condition. In one embodiment, the method can be performed by introducing a polynucleotide portion of plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cell to a stress condition.

The polynucleotide portion of the plant stress-regulated gene can encode a stress-regulated polypeptide or functional peptide portion thereof (see SEQ ID NOS:1-2703), wherein expression of the stress-regulated polypeptide or functional peptide portion thereof either increases the stress tolerance of the transgenic plant, or decreases the stress tolerance of the transgenic plant. The polynucleotide portion of the plant stress-regulated gene encoding the stress-regulated polypeptide or functional peptide portion thereof can be operatively linked to a heterologous promoter. The polynucleotide portion of the plant stress-regulated gene also can comprise a stress-regulated gene regulatory element (see SEQ ID NOS:2704-5379). The stress-regulated gene regulatory element can integrate into the plant cell genome in a site-specific manner, whereupon it can be operatively linked to a heterologous nucleotide sequence, which can be expressed in response to a stress condition specific for the regulatory element; or can be a mutant regulatory element, which is not responsive to the stress condition, whereby upon integrating into the plant cell genome, the mutant regulatory element disrupts an endogenous stress-regulated regulatory element of a plant stress-regulated gene, thereby altering the responsiveness of the plant stress-regulated gene to the stress condition.

In one aspect, the invention provides a method for producing a transgenic plant by introducing into at least one plant cell a recombinant nucleic acid construct comprising i) all or a portion of any one of SEQ ID NOS:1-5379; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to all or a portion of the complement of any one of SEQ ID NOS:1-2703; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to abiotic stress, and that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2704-5379; iv) a polynucleotide having at least 90% sequence identity with any one of SEQ ID NO:1-5379; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv), wherein the fragment comprises a nucleotide sequence that alters transcription of an operatively linked coding region in response to abiotic stress; and regenerating a plant from the at least one plant cell.

Another aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:1-1261 or 2704-3955; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:1-1261; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to cold stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2704-3955; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:1-1261 or 2704-3955; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv) wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to cold stress; and regenerating a plant from the at least one plant cell.

In another aspect, the invention provides a method for producing a transgenic plant by introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:2428-2585 or 5108-5263; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2428-2585; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to osmotic stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:5108-5263; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:2428-2585 or 5108-5263; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv), wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to osmotic stress; and regenerating a plant from the at least one plant cell.

Still another aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:2227-2427 or 4910-5107; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2227-2427; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to saline stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2227-2427; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:4910-5107; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv) wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to saline stress; and regenerating a plant from the at least one plant cell.

Yet another aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:1699-1969 or 4389-4654; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:1699-1969; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to a combination of cold and osmotic stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:4389-4654; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:1699-1969 or 4389-4654; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv), wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to a combination of cold and osmotic stress; and regenerating a plant from the at least one plant cell.

Yet another aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:1970-2226 or 4655-4909; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:1970-2226; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to a combination of cold and saline stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:4655-4909; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:1970-2226 or 4655-4909; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv), wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to a combination of cold and saline stress; and regenerating a plant from the at least one plant cell.

A further aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:2586-2703 or 5264-5379; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:2586-2703; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to a combination of osmotic and saline stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS: 5264-5379; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:2586-2703 or 5264-5379; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv), wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to a combination of osmotic and saline stress; and regenerating a plant from the at least one plant cell.

Another aspect provides a method for producing a transgenic plant comprising introducing into at least one plant cell a recombinant nucleic acid construct comprising i) any one of SEQ ID NOS:1262-1698 or 3956-4388; ii) a polynucleotide comprising a coding region that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:1262-1698; iii) a polynucleotide comprising a sequence that alters transcription of an operatively linked coding region in response to a combination of cold, osmotic and saline stress that hybridizes under conditions of high stringency to the complement of any one of SEQ ID NOS:3956-4388; iv) a polynucleotide that has at least 90% sequence identity with any one of SEQ ID NOS:1262-1698 or 3956-4388; v) a fragment of any one of the sequences of iv), wherein the fragment comprises a coding region; or vi) a fragment of any one of the sequences of iv) wherein the fragment comprises a sequence or region that alters transcription of an operatively linked coding region in response to a combination of cold, osmotic and saline stress; and regenerating a plant from the at least one plant cell. Further aspects include plants and uniform populations of plants made by the above methods as well as seeds and progeny from such plants.

In another embodiment, a transgene introduced into a plant cell according to a method of the invention can encode a polypeptide that regulates expression from an endogenous plant stress-regulated gene. Such a polypeptide can be, for example, a recombinantly produced polypeptide comprising a zinc finger domain, which is specific for the regulatory element, and an effector domain, which can be a repressor domain or an activator domain. The polynucleotide encoding the recombinant polypeptide can be operatively linked to and expressed from a constitutively active, inducible or tissue specific or phase specific regulatory element. Expression of the recombinant polypeptide from a plant stress-regulated promoter as disclosed herein can be particularly advantageous in that the polypeptide can be coordinately expressed with the endogenous plant stress-regulated genes upon exposure to a stress condition. The invention also provides transgenic plants produced by a method as disclosed, as well as to a plant cell obtained from such transgenic plant, wherein said plant cell exhibits altered responsiveness to the stress condition; a seed produced by the transgenic plant; and a cDNA or genomic DNA library prepared from the transgenic plant, or from a plant cell from said transgenic plant, wherein said plant cell exhibits altered responsiveness to the stress condition.

In one aspect, the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence substantially similar to a sequence of any one of SEQ ID NOS:2704-5379, which can alter transcription of an operatively linked polynucleotide in a plant cell in response to an abiotic stress. Additional aspects of the invention provide isolated polynucleotides, including, for example, sequences substantially similar to any of SEQ ID NOS:2704-3955, which can alter transcription of an operatively linked polynucleotide in response to a cold stress; isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:5108-5263, which can alter transcription of an operatively linked polynucleotide in response to an osmotic stress; isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:4910-5107, which can alter transcription of an operatively linked polynucleotide in response to a saline stress; isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:4389-4654, which can alter transcription of an operatively linked polynucleotide in response to a combination of cold and osmotic stresses; isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:4655-4909, which can alter transcription of an operatively linked polynucleotide in response to a combination of cold and saline stresses; isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:5264-5379, which can alter transcription of an operatively linked polynucleotide in response to a combination of osmotic and saline stresses; and isolated polynucleotides substantially similar to a sequence of any of SEQ ID NOS:3956-4388, which can alter transcription of an operatively linked polynucleotide in response to a combination of cold, osmotic and saline stresses.

Related aspects of the invention provide an isolated nucleotide sequences that can alter transcription of an operatively linked polynucleotide in response to an abiotic stress, and that hybridize under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:2704-5379. Additional aspects provide an isolated nucleotide sequence that can alter transcription of an operatively linked polynucleotide in response to cold stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:2704-3955; a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to osmotic stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:5108-5263; a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to saline stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:4910-5107; a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to a combination of cold and osmotic stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:4389-4654; a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to a combination of cold and saline stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:4655-4909; a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to an combination of osmotic and saline stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:5264-5379; and a nucleotide sequence that alters transcription of an operatively linked polynucleotide in response to a combination of cold, osmotic and saline stress, and that hybridizes under stringent conditions, preferably highly stringent conditions, to the complement of any one of SEQ ID NOS:3956-4388.

Further aspects provide an expression cassette comprising as operatively linked components any of the above isolated nucleic acid sequences that alter transcription, a coding region, and a termination sequence. Also provided are host cells and seeds comprising such expression cassettes, plants containing such host cells and seeds and progeny of plants containing said host cells. In related aspects, the coding region of the expression cassettes comprise sequences encoding marker proteins and sequences involved in gene silencing such as antisense sequences, double stranded RNAi sequences, a triplexing agent, and sequences comprising dominant negative mutations. In additional related aspects, the coding regions comprise sequences encoding polypeptides that alter the response of a plant to an abiotic stress.

The present invention also relates to a method of modulating the responsiveness of a plant cell to a stress condition. Such a method can be performed, for example, by introducing a polynucleotide portion of a plant stress-regulated genes described herein into the plant cell, thereby modulating the responsiveness of the plant cell to a stress condition. Such a method can result in the responsiveness of the plant cell being increased upon exposure to the stress condition, which, in turn, can result in increased or decreased tolerance of the plant cell to a stress condition; or can result in the responsiveness of the plant cell to the stress condition being decreased, which, in turn, can result in increased or decreased tolerance of the plant cell to a stress condition. In one embodiment, the polynucleotide portion of the plant stress-regulated gene can integrate into the genome of the plant cell, thereby modulating the responsiveness of the plant cell to the stress condition. In another embodiment, the polynucleotide portion of the plant stress-regulated gene encodes a stress-regulated polypeptide or functional peptide portion thereof, and can be operatively linked to a heterologous promoter. The polynucleotide portion of the plant stress-regulated gene also can contain a mutation, whereby upon integrating into the plant cell genome, the polynucleotide disrupts (knocks-out) an endogenous plant stress-regulated sequence, thereby modulating the responsiveness of the plant cell to the stress condition. Depending on whether the knocked-out gene encodes an adaptive or a maladaptive stress-regulated polypeptide, the responsiveness of the plant will be modulated accordingly.

The present invention further relates to a method of modulating the activity of a biological pathway in a plant cell, wherein the pathway involves a stress-regulated polypeptide or a non-protein regulatory molecule. Such a method can be performed by introducing a polynucleotide portion of a plant stress-regulated gene, or a polynucleotide derived therefrom, for example a ribozyme derived from a nucleotide sequence as set forth in any of SEQ ID NOS:1-2703, into the plant cell, thereby modulating the activity of the biological pathway. The method can be performed with respect to a pathway involving any of the stress-regulated polypeptides as disclosed herein or encoded by the polynucleotides disclosed herein, as well as using homologs or orthologs thereof. In one embodiment, the method is performed by introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene comprises a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the activity of the biological pathway.

The present invention also relates to a method of identifying a polynucleotide that modulates a stress response in a plant cell. In one embodiment the method comprises determining gene expression in a plant exposed to at least one stress to produce an expression profile and identifying sequences whose expression is altered at least two fold compared to plants not exposed to the stress. Such an expression profile can be obtained, for example, by contacting an array of probes representative of a plant cell genome with nucleic acid molecules expressed in a plant cell exposed to the stress; and detecting one or more nucleic acid molecules expressed at a level different from a level of expression in the absence of the stress. The method can further comprise introducing the differentially expressed nucleic acid molecule into a plant cell; and detecting a modulated response of the genetically modified plant cell to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell. The stress can be any stress, for example, an abiotic stress such as exposure to an abnormal level of cold, osmotic pressure, and salinity. The contacting is under conditions that allow for selective hybridization of a nucleic acid molecule with probe having sufficient complementarity, for example, under stringent hybridization conditions. Expression of the nucleic acid molecule can increase or decrease the tolerance of the plant cell to the stress, and the nucleic acid molecule can be expressed at a level that is less than or greater than the level of expression in the absence of the stress.

In still another embodiment, the polynucleotide portion of the plant stress-regulated gene can comprise a stress-regulated regulatory element, which can be operatively linked to a heterologous nucleotide sequence, the expression of which can modulate the responsiveness of the plant cell to a stress condition. Such a heterologous nucleotide sequence can encode, for example, a stress-inducible transcription factor such as DREBIA. The heterologous nucleotide sequence also can encode a polynucleotide that is specific for a plant stress-regulated gene, for example, an antisense molecule, an RNAi molecule, a ribozyme, and a triplexing agent, any of which, upon expression in the plant cell, reduces or inhibits expression of a stress-regulated polypeptide encoded by the gene, thereby modulating the responsiveness of the plant cell to a stress condition, for example, an abnormal level of cold, osmotic pressure, and salinity. In another aspect, the method can include introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene includes a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the responsiveness of the plant cell to a stress condition. The invention also relates to a plant cell obtained by any of the methods of modulating the responsiveness of a plant to a stress condition or combination of stress conditions, and to a plant comprising such a plant cell.

The present invention further relates to a method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, such a method being useful for marker-assisted breeding. Such a method can be performed, for example, by contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probes that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-5379; detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition. For example, the abiotic stress condition can be cold stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-1261 and 2704-3955, for example, at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, 2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, and 3313-3955; or the abiotic stress condition can be saline stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427 and 4910-5107; or the abiotic stress condition can be osmotic stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2428-2585 and 5108-5263. In addition, a combination of abiotic stress conditions can be a combination of cold stress and osmotic stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1669-1969 and 4389-4654, for example, at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1725, 1727-1865, 1867-1917, 1919-1927, 1929-1969, 4389-4414, 4416-4552, 4554-4602, 4604-4612, and 4613-4654; or the combination of abiotic stress conditions can be a combination of cold stress and saline stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226 and 4655-4909; or the combination of abiotic stress conditions can be a combination of osmotic stress and saline stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703 and 5264-5379; or the combination of abiotic stress conditions can be a combination of cold stress, osmotic stress and saline stress, and the nucleic acid probe can include at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698 and 3956-4388, for example, at least about 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1698, 3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, and 4326-4388.

The present invention also relates to a method of expressing a heterologous nucleotide sequence in a plant cell. Such a method can be performed, for example, by introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, whereby, upon exposure of the plant cell to a stress condition, the heterologous nucleotide sequence is expressed in the plant cell. In one embodiment, the stress-regulated gene regulatory element is any of the sequences described herein that are capable of altering transcription of an operatively linked sequence in response to an abiotic stress, for example, SEQ ID NOS:2704-5379. In another embodiment, stress-regulated gene regulatory element comprises a nucleotide sequence as set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell. The heterologous nucleotide sequence can encode a selectable marker, a diagnostic marker, or a polypeptide that confers a desirable trait upon the plant cell, for example, a polypeptide that improves the nutritional value, digestibility or ornamental value of the plant cell, or a plant comprising the plant cell.

The present invention additionally relates to a method of identifying a stress condition to which a plant cell was exposed by comparing an expression profile from a test plant suspected of having been exposed to at least one stress condition to an expression profile obtained from a reference plant, preferably of the same species, which has been exposed to the suspected stress condition. Such a method can be performed, for example, by contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein the probe comprises at least 15 nucleotides of a plant stress-regulated gene, wherein the stress-regulated gene does not have a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, or a nucleotide sequence complementary thereto, whereby detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress, and whereby an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress. For example, the abiotic stress is cold stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261 or a nucleotide sequence complementary thereto; or the abiotic stress can be a saline stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427 or a nucleotide sequence complementary thereto; or the abiotic stress can be an osmotic stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in two or more of SEQ ID NOS:2428-2585 or a nucleotide sequence complementary thereto.

A method of identifying a stress condition to which a plant cell was exposed also can be performed, for example, by contacting nucleic acid molecules expressed in the test plant cell with an array of probes representative of the plant cell genome; detecting a profile of expressed nucleic acid molecules characteristic of a stress response, and comparing the expression pattern in the test plant to the expression pattern obtained from a reference plant thereby identifying the stress condition to which the plant cell was exposed. The contacting is under conditions that allow for selective hybridization of a nucleic acid molecule with probes having sufficient complementarity, for example, under stringent hybridization conditions. The profile can be characteristic of exposure to a single stress condition, for example, an abnormal level of cold, osmotic pressure, or salinity, or can be characteristic of exposure to more than one stress condition, for example, cold, increased osmotic pressure and increased salinity. In one embodiment, the nucleotide sequence of a gene whose expression is detected is selected from a polynucleotide comprising any of SEQ ID NOS:1-2703. In further embodiments, the nucleotide sequence of a gene that is expressed in response a particular stress or combination of stresses can comprise a polynucleotide expressed in response to cold stress (SEQ ID NOS:1-1261), osmotic stress (SEQ ID NOS:2428-2585), saline (salt) stress (SEQ ID NOS:2227-2427), a combination of cold and osmotic stress (SEQ ID NOS:1699-1969), a combination of saline and osmotic stress (SEQ ID NOS:1970-2226), a combination of osmotic and saline stress (SEQ ID NOS:2586-2703), or a combination of cold, osmotic and saline stress (SEQ ID NOS:1262-1698).

In another embodiment, the method can be used for determining whether a test plant has been exposed to a combination of abiotic stress conditions. Such a method can be performed, for example, by contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, whereby detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions. For example, the combination of abiotic stress conditions can be a combination of a cold stress and an osmotic stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1969, or a nucleotide sequence complementary thereto; or the combination of abiotic stress conditions can be a combination of a cold stress and a saline stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226, or a nucleotide sequence complementary thereto; or the combination of abiotic stress conditions can be a combination of an osmotic stress and a saline stress, and the probe can included at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703, or a nucleotide sequence complementary thereto; or the combination of abiotic stress conditions can be a combination of a cold stress, a saline stress and an osmotic stress, and the probe can include at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698, or a nucleotide sequence complementary thereto.

The present invention also relates to a method for monitoring a population of plants for exposure to a stress condition or combination of stress conditions. Such a method can be performed, for example, by introducing into the population of a plants a sentinel plant, wherein said sentinel plant is a transgenic plant, which contains plant cells containing a stress-regulated regulatory element operatively linked to a polynucleotide encoding a detectable marker; and examining the sentinel plant for expression of the detectable marker, which is indicative of exposure of the population of plants to a stress condition or combination of stress conditions. The stress condition or combination of stress conditions can be any such condition or conditions, particularly an abiotic stress condition or combination of abiotic stress conditions. The detectable marker can be any reporter molecule that is readily or conveniently detectable, particularly a marker that is visibly detectable, for example, a luminescent detectable marker such as luciferin, or a fluorescent detectable marker such as a green fluorescent protein, a yellow fluorescent protein, a cyan fluorescent protein, a red fluorescent protein, or an enhanced or modified form thereof.

The present invention further relates to a transgenic plant, which contains a nucleic acid construct comprising a polynucleotide portion of plant stress-regulated polynucleotide. In one embodiment, the transgenic plant exhibits altered responsiveness to a stress condition as compared to a corresponding reference plant not containing the construct. Such a transgenic plant can contain, for example, a construct that disrupts an endogenous stress-regulated gene in the plant, thereby reducing or inhibiting expression of the gene in response to a stress condition. Such a knock-out can increase or decrease tolerance of the plant to a stress condition. The transgene also can comprise a coding sequence of a plant stress-regulated gene, which can be operatively linked to a heterologous regulatory element such as a constitutively active regulatory element, an regulated regulatory element, a tissues specific or phase specific regulatory element, or the like. In another embodiment, the transgenic plant contains a nucleic acid construct comprising a plant stress-regulated regulatory element, which can be operatively linked to a heterologous nucleotide sequence that can encode a polypeptide. Expression of the heterologous polypeptide can confer a desirable characteristic on the plant, for example, can improve the nutritional or ornamental value of the transgenic plant. In still another embodiment, the transgenic plant contains multiple nucleic acid constructs, which can be multiple copies of the same construct, or can be two or more different constructs.

The present invention also relates to a plant stress-regulated regulatory element, which is obtained from a plant stress-regulated polynucleotide disclosed herein for example any of SEQ ID NOS:2704-5379; a homolog or ortholog thereof. The invention also provides a method of identifying an agent, for example a transcription factor, that specifically binds to or activates a plant stress-regulated regulatory element. Such a method can be performed, for example, by contacting the regulatory element with a plant cell extract, and identifying polypeptides that specifically bind to the regulatory element. Confirmation that the specifically binding polypeptide is a transcription factor can be demonstrated using, for example, the stress-regulated regulatory element operably linked to a reporter gene, and detecting expression of the reporter gene. Control constructs comprising a regulatory element, other than a plant stress-regulated regulatory element, operatively linked to a reporter molecule can be used to confirm that the transcription factor is specific for the plant stress-regulated regulatory element. A polynucleotide encoding such a transcription factor also can be obtained.

The present invention also relates to a method of using a polynucleotide portion of a plant stress-regulated gene to confer a selective advantage on a plant cell. In one embodiment, such a method is performed by introducing a plant stress-regulated regulatory element into a plant cell such as those described herein, wherein, upon exposure of the plant cell to a stress condition to which the regulatory element is responsive, a nucleotide sequence operatively linked to the regulatory element is expressed, thereby conferring a selective advantage to plant cell. The operatively linked nucleotide sequence can be, for example, a transcription factor, the expression of which induces the further expression of polynucleotides involved in a stress response, thereby enhancing the response of a plant to the stress condition. In another embodiment, a coding sequence of a plant stress-regulated gene as disclosed herein is introduced into the cell, thereby providing the plant with a selective advantage in response to a stress condition. In still another embodiment, the method results in the knock-out of a plant stress-regulated gene as disclosed herein in a first population of plants, thereby providing a selective advantage to a stress condition in a second population of plants.

The invention further relates to a method of identifying an agent that modulates the activity of a stress-regulated regulatory element of a plant. In a particular embodiment, is provided a method for identifying an agent that alters the activity of an abiotic stress responsive regulatory element comprising contacting the agent or a composition containing an agent to be tested with at least one abiotic stress responsive regulatory element, preferably selected from the group consisting of SEQ ID NOS:2704-5379 (see Table 2), and determining the effect of the agent on the ability of the regulatory sequence to regulate transcription. In further embodiments, the regulatory elements are associated with particular stresses or combination of stresses such as cold stress (SEQ ID NOS:2704-3955), osmotic stress (SEQ ID NOS:5108-5263), saline stress (SEQ ID NOS:4910-5107), a combination of cold and osmotic stress (SEQ ID NOS:4389-4654), a combination of cold and saline stress (SEQ ID NOS:4655-4909), a combination of osmotic and saline stress (SEQ ID NOS:5264-5379), or a combination of cold, osmotic and saline stress (SEQ ID NOS:3956-4388). In one embodiment, the regulatory element can be operatively linked to a heterologous polynucleotide encoding a reporter molecule, and an agent that modulates the activity of the stress-regulated regulatory element can be identified by detecting a change in expression of the reporter molecule due to contacting the regulatory element with the agent. Such a method can be performed in vitro in a plant cell-free system, or in a plant cell in culture or in a plant in situ. In another embodiment, the agent is contacted with a transgenic plant containing an introduced plant stress-regulated regulatory element, and an agent that modulates the activity of the regulatory element is identified by detecting a phenotypic change in the transgenic plant. The methods of the invention can be performed in the presence or absence of the stress condition to which the particularly regulatory element is responsive.

Another aspect provides a method for identifying an agent that alters abiotic stress responsive polynucleotide expression in a plant or plant cell comprising contacting a plant or plant cell with a test agent; subjecting the plant cell or plant cell to an abiotic stress or combination of stresses before, during or after contact with the agent to be tested; obtaining an expression profile of the plant or plant cell and comparing the expression profile of the plant or plant cell to an expression profile from a plant or plant cell not exposed to the abiotic stress or combination of stresses. In one embodiment, the expression profile comprises expression data for at least one nucleotide sequence comprising any of SEQ ID NOS:1-5379 (see Tables 1 and 2). In additional embodiments, the expression profile comprises expression data for at least one, and preferably two or more sequences associated with a particular abiotic stress or combination of stresses such as cold stress (SEQ ID NOS:1-1261 and 2704-3955), osmotic stress (SEQ ID NOS:2428-2585 and 5108-5263), saline stress (SEQ ID NOS:2227-2427 and 4910-5107), a combination of cold and osmotic stress (SEQ ID NOS:1699-1969 and 4389-4654), a combination of cold and saline stress (SEQ ID NOS:1970-2226 and 4655-4909), a combination of osmotic and saline stress (SEQ ID NOS:2586-2703 and 5264-5379), or a combination of cold, osmotic and saline stress (SEQ ID NOS:1262-1698 and 3956-4388).

Still another aspect provides nucleotide probes useful for detecting an abiotic stress response in plants, the probes comprising a nucleotide sequence of at least 15, 25, 50 or 100 nucleotides that hybridizes under stringent, preferably highly stringent, conditions to at least one sequence comprising any of SEQ ID NOS:1-2703. Also provided are nucleotide probes comprising at least 15, 25, 50 or 100 nucleotides in length that hybridize under stringent, preferably highly stringent conditions, to at least one gene associated with a particular stress or combination of stresses, for example cold stress, (SEQ ID NOS:1-1261), osmotic stress (SEQ ID NOS:2428-2585), saline stress (SEQ ID NOS:2227-2427), a combination of cold and osmotic stress (SEQ ID NOS:1699-1969), a combination of cold and saline stress (SEQ ID NOS:1970-2226), a combination of osmotic and saline stress (SEQ ID NOS:2586-2703), or a combination of cold, osmotic, and saline stress (SEQ ID NOS:1262-1698).

An additional aspect provides a method for marker-assisted breeding to select plants having an altered resistance to abiotic stress comprising obtaining nucleic acid molecules from the plants to be selected; contacting the nucleic acid molecules with one or more probes that selectively hybridize under stringent, preferably highly stringent, conditions to a nucleic acid sequence selected from the group consisting of SEQ ID NOS:1-2703; detecting the hybridization of the one or more probes to the nucleic acid sequences wherein the presence of the hybridization indicates the presence of a gene associated with altered resistance to abiotic stress; and selecting plants on the basis of the presence or absence of such hybridization. Marker-assisted selection can also be accomplished using one or more probes which selectively hybridize under stringent, preferably highly stringent conditions, to a nucleotide sequence comprising a polynucleotide expressed in response associated with a particular stress, for example, a nucleotide sequence comprising any of SEQ ID NOS:1-1261 (cold stress), SEQ ID NOS:2428-2585 (osmotic stress), SEQ ID NOS:2227-2427 (saline stress), SEQ ID NOS:1699-1969 (cold and osmotic stress), SEQ ID NOS:1970-2226 (cold and saline stress), SEQ ID NOS:2586-2703 (osmotic and saline stress), or SEQ ID NOS:1262-1698 (cold, osmotic and saline stress). In each case marker-assisted selection can be accomplished using a probe or probes to a single sequence or multiple sequences. If multiple sequences are used they can be used simultaneously or sequentially.

A further aspect provides a method for monitoring a population of plants comprising providing at least one sentinel plant containing a recombinant polynucleotide comprising a stress responsive regulatory sequence selected from the group consisting of SEQ ID NOS:2704-5379 which is operatively linked to a nucleotide sequence encoding a detectable marker, for example a fluorescent protein. Additional aspects provide the use of various regulatory sequences including those associated with cold stress (SEQ ID NOS:2704-3955), osmotic stress (SEQ ID NOS:5108-5263), saline stress (SEQ ID NOS:4910-5107), cold and osmotic stress (SEQ ID NOS:4389-4654), cold and saline stress (SEQ ID NOS:4655-4909), osmotic and saline stress (SEQ ID NOS:5264-5379), and cold, osmotic and saline stress (SEQ ID NOS:3956-4388), or fragments thereof wherein such fragments can alter transcription of an operatively linked nucleotide sequence in response to an abiotic stress.

A further aspect provides a computer readable medium having stored thereon computer executable instructions for performing a method comprising receiving data on gene expression in a test plant of at least one nucleic acid molecule having at least 70%, preferably at least 80%, more preferably at least 90%, and most preferably at least 95% nucleotide sequence identity to one or more polynucleotide sequences as set forth in any of SEQ ID NOS:1-2703; and comparing expression data from the test plant to expression data for the same polynucleotide sequence or sequences in a plant that has been exposed to at least one abiotic stress.

Yet a further aspect provides a computer readable medium having stored thereon a data structure comprising, sequence data for at least one, and preferably a plurality of nucleic acid molecules having at least 70%, preferably at least 80%, more preferably at least 90%, and most preferably at least 95% nucleotide sequence identity to a polynucleotide comprising any of SEQ ID NOS:1-2703, or the complement thereof; and a module receiving the nucleic acid molecule sequence data which compares the nucleic acid molecule sequence data to at least one other nucleic acid sequence.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to clusters of genes that are induced in response to one or a combination of abiotic stress conditions. Abiotic stress conditions, such as a shortage or excess of solar energy, water and nutrients, and salinity, high and low temperature, or pollution (e.g., heavy metals), can have a major impact on plant growth and can significantly reduce the yield, for example, of cultivars. Under conditions of abiotic stress, the growth of plant cells is inhibited by arresting the cell cycle in late G1, before DNA synthesis, or at the G2/M boundary (see Dudits, Plant Cell Division, Portland Press Research, Monograph; Francis, Dudits, and Inze, eds., 1997; chap. 2, page 21; Bergounioux, Protoplasma 142:127-136, 1988). The identification of stress-regulated gene clusters, using microarray technology, provides a means to identify plant stress-regulated genes.

As used herein, the term “cluster,” when used in reference to stress-regulated genes, refers to nucleotide sequences of genes that have been selected by drawing Venn diagrams, and selecting those genes that are regulated only by a selected stress condition. In general, a cluster of stress-regulated genes includes at least 5, 10, 15, or 20 genes, including polynucleotide portions thereof, each of which is responsive to the same selected stress condition or conditions. The selected stress condition can be a single stress condition, for example, cold, osmotic stress or salinity stress (see Tables 3-14), or can be a selected combination of stress conditions, for example, cold, osmotic stress and salinity stress (see Tables 15-26). In addition, a cluster can be selected based on specifying that all of the genes are coordinately regulated, for example, they all start at a low level and are induced to a higher level. However, a cluster of saline stress-regulated genes, for example, that was selected for coordinate regulation from low to high, also can be decreased in response to cold or mannitol. By varying the parameters used for selecting a cluster of gene nucleotide sequences, those genes that are expressed in a specific manner following a stress can be identified.

As used herein in reference to a polynucleotide or polynucleotide portion of a gene or nucleic acid molecule, the term “isolated” means a polynucleotide, polynucleotide portion of a gene, or nucleic acid molecule that is free of one or both of the nucleotide sequences that normally flank the polynucleotide in a genome of a naturally-occurring organism from which the polynucleotide is derived. The term includes, for example, a polynucleotide or fragment thereof that is incorporated into a vector or expression cassette; into an autonomously replicating plasmid or virus; into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule independent of other polynucleotides. It also includes a recombinant polynucleotide that is part of a hybrid polynucleotide, for example, one encoding a polypeptide sequence.

The terms “polynucleotide,” “oligonucleotide,” and “nucleic acid sequence” are used interchangeably herein to refer to a polymeric (2 or more monomers) form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Although nucleotides are usually joined by phosphodiester linkages, the term also includes polymers containing neutral amide backbone linkages composed of aminoethyl glycine units. The terms are used only to refer to the primary structure of the molecule. Thus, the term includes double stranded and single stranded DNA molecules, including a sense strand or an antisense strand, and RNA molecules as well as genomic DNA, cDNA, mRNA and the like. It will be recognized that such polynucleotides can be modified, for example, by including a label such as a radioactive, fluorescent or other tag, by methylation, by the inclusion of a cap structure, by containing a substitution of one or more of the naturally occurring nucleotides with a nucleotide analog, by containing an internucleotide modification such as having uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, or the like), by containing a pendant moiety such as a protein (e.g., a nuclease, toxin, antibody, signal peptide, poly-L-lysine, or the like), by containing an intercalator such as acridine or psoralen, by containing a chelator, which can be a metal such as boron, an oxidative metal, or a radioactive metal, by containing an alkylator, or by having a modified linkage (e.g., an alpha anomeric nucleic acid).

The term “recombinant nucleic acid molecule” refers to a polynucleotide produced by human intervention. A recombinant nucleic acid molecule can contain two or more nucleotide sequences that are linked in a manner such that the product is not found in a cell in nature. In particular, the two or more nucleotide sequences can be operatively linked and, for example, can encode a fusion polypeptide, or can comprise a nucleotide sequence and a regulatory element. A recombinant nucleic acid molecule also can be based on, but different, from a naturally occurring polynucleotide, for example, a polynucleotide having one or more nucleotide changes such that a first codon, which normally is found in the polynucleotide, is replaced with a degenerate codon that encodes the same or a conservative amino acid, or such that a sequence of interest is introduced into the polynucleotide, for example, a restriction endonuclease recognition site or a splice site, a promoter, a DNA replication initiation site, or the like.

As used herein, the term “abiotic stress” or “abiotic stress condition” refers to the exposure of a plant, plant cell, or the like, to a non-living (“abiotic”) physical or chemical agent or condition that has an adverse effect on metabolism, growth, development, propagation and/or survival of the plant (collectively “growth”). An abiotic stress can be imposed on a plant due, for example, to an environmental factor such as water (e.g., flooding, drought, dehydration), anaerobic conditions (e.g., a low level of oxygen), abnormal osmotic conditions, salinity or temperature (e.g., hot/heat, cold, freezing, frost), a deficiency of nutrients or exposure to pollutants, or by a hormone, second messenger or other molecule. Anaerobic stress, for example, is due to a reduction in oxygen levels (hypoxia or anoxia) sufficient to produce a stress response. A flooding stress can be due to prolonged or transient immersion of a plant, plant part, tissue or isolated cell in a liquid medium such as occurs during monsoon, wet season, flash flooding or excessive irrigation of plants, or the like. A cold stress or heat stress can occur due to a decrease or increase, respectively, in the temperature from the optimum range of growth temperatures for a particular plant species. Such optimum growth temperature ranges are readily determined or known to those skilled in the art. Dehydration stress can be induced by the loss of water, reduced turgor, or reduced water content of a cell, tissue, organ or whole plant. Drought stress can be induced by or associated with the deprivation of water or reduced supply of water to a cell, tissue, organ or organism. Saline stress (salt stress) can be associated with or induced by a perturbation in the osmotic potential of the intracellular or extracellular environment of a cell. Osmotic stress also can be associated with or induced by a change, for example, in the concentration of molecules in the intracellular or extracellular environment of a plant cell, particularly where the molecules cannot be partitioned across the plant cell membrane.

As disclosed herein, clusters of plant stress-regulated genes (Example 1; see, also, Tables 1-31) and homologs and orthologs thereof (Table 32) have been identified. Remarkably, several of the stress-regulated genes previously were known to encode polypeptides having defined cellular functions, including roles as transcription factors, enzymes such as kinases, and structural proteins such as channel proteins (see Tables 29-31). The identification of Arabidopsis stress-regulated genes provides a means to identify homologous and orthologous genes and gene sequences in other plant species using well known procedures and algorithms based on identity (or homology) to the disclosed sequences. Thus, the invention provides polynucleotide sequences comprising plant stress-regulated genes that are homologs or orthologs, variants, or otherwise substantially similar to the polynucleotides disclosed herein, and having an E value≦1×10⁻⁸, which can be identified, for example, by a BLASTN search using the Arabidopsis polynucleotides of Tables 1 and 2 (SEQ ID NOS:1-5379) as query sequences (see Table 32, on CD).

A polynucleotide sequence of a stress-regulated gene as disclosed herein can be particularly useful for performing the methods of the invention on a variety of plants, including but not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea ultilane), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, duckweed (Lemna), barley, tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals such as azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum are also included. Additional ornamentals within the scope of the invention include impatiens, Begonia, Pelargonium, Viola, Cyclamen, Verbena, Vinca, Tagetes, Primula, Saint Paulia, Agertum, Amaranthus, Antihirrhinum, Aquilegia, Cineraria, Clover, Cosmo, Cowpea, Dahlia, Datura, Delphinium, Gerbera, Gladiolus, Gloxinia, Hippeastrum, Mesembryanthemum, Salpiglossos, and Zinnia. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga ultilane); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis).

Leguminous plants which may be used in the practice of the present invention include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mung bean, lima bean, fava bean, lentils, chickpea, etc. Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo. Preferred forage and turf grass for use in the methods of the invention include alfalfa, orchard grass, tall fescue, perennial ryegrass, creeping bent grass, and redtop.

Other plants within the scope of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, ultilan sprouts, onion, carrot, leek, beet, broad bean, celery, radish, pumpkin, endive, gourd, garlic, snapbean, spinach, squash, turnip, ultilane, chicory, groundnut and zucchini.

As used herein, the term “substantially similar”, when used herein with respect to a nucleotide sequence, means a nucleotide sequence corresponding to a reference nucleotide sequence, wherein the corresponding sequence encodes a polypeptide or comprises a regulatory element having substantially the same structure and function as the polypeptide encoded by the reference nucleotide sequence, for example, where only changes in amino acids not affecting the polypeptide function occur. For purposes of the present invention, a reference (or query) sequence is a polynucleotide sequence as set forth in any of SEQ ID NOS:1-2703 or a polypeptide encoded thereby. Desirably, a substantially similar nucleotide sequence encodes the polypeptide encoded by the reference nucleotide sequence. The percentage of identity between the substantially similar nucleotide sequence and the reference nucleotide sequence desirably is at least 60%, more desirably at least 75%, preferably at least 90%, more preferably at least 95%, still more preferably at least 99% and including 100%. A nucleotide sequence is “substantially similar” to reference nucleotide sequence hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 2×SSC, 0.1% SDS at 50° C., more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C. (stringent conditions), more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.5×SSC, 0.1% SDS at 50° C. (high stringency), preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 50° C. (very high stringency), more preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 65° C. (extremely high stringency).

In addition, the term “substantially similar,” when used in reference to a polypeptide sequence, means that an amino acid sequence relative to a reference (query) sequence shares at least about 65% amino acid sequence identity, particularly at least about 75% amino acid sequence identity, and preferably at least about 85%, more preferably at least about 90%, and most preferably at least about 95% or greater amino acid sequence identity. Generally, sequences having an E≦10⁻⁸ are considered to be substantially similar to a query sequence. Such sequence identity can take into account conservative amino acid changes that do not substantially affect the function of a polypeptide. As such, homologs or orthologs of the Arabidopsis stress-regulated nucleotide sequences disclosed herein, variants thereof, and polypeptides substantially similar to the polynucleotide sequence of Arabidopsis stress-regulated genes set forth in SEQ ID NOS:1-5379 are encompassed within the present invention and, therefore, useful for practicing the methods of the invention (see, for example, Table 32, which is on the CD-R filed herewith, and incorporated herein by reference).

Homology or identity is often measured using sequence analysis software such as the Sequence Analysis Software Package of the Genetics Computer Group (University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). Such software matches similar sequences by assigning degrees of homology to various deletions, substitutions and other modifications. The terms “homology” and “identity,” when used herein in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or of nucleotides that are the same when compared and aligned for maximum correspondence over a comparison window or designated region as measured using any number of sequence comparison algorithms or by manual alignment and visual inspection.

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

The term “comparison window” is used broadly herein to include reference to a segment of any one of the number of contiguous positions, for example, about 20 to 600 positions, for example, amino acid or nucleotide position, usually about 50 to about 200 positions, more usually about 100 to about 150 positions, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequence for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, for example, by the local homology algorithm of Smith and Waterman (Adv. Appl. Math. 2:482, 1981), by the homology alignment algorithm of Needleman and Wunsch (J. Mol. Biol. 48:443, 1970), by the search for similarity method of Person and Lipman (Proc. Natl. Acad. Sci., USA 85:2444, 1988), each of which is incorporated herein by reference; by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.); or by manual alignment and visual inspection. Other algorithms for determining homology or identity include, for example, in addition to a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information), ALIGN, AMAS (Analysis of Multiply Aligned Sequences), AMPS (Protein Multiple Sequence Alignment), ASSET (Aligned Segment Statistical Evaluation Tool), BANDS, BESTSCOR, BIOSCAN (Biological Sequence Comparative Analysis Node), BLIMPS (BLocks IMProved Searcher), FASTA, Intervals & Points, BMB, CLUSTAL V, CLUSTAL W, CONSENSUS, LCONSENSUS, WCONSENSUS, Smith-Waterman algorithm, DARWIN, Las Vegas algorithm, FNAT (Forced Nucleotide Alignment Tool), Framealign, Framesearch, DYNAMIC, FILTER, FSAP (Fristensky Sequence Analysis Package), GAP (Global Alignment Program), GENAL, GIBBS, GenQuest, ISSC (Sensitive Sequence Comparison), LALIGN (Local Sequence Alignment), LCP (Local Content Program), MACAW (Multiple Alignment Construction & Analysis Workbench), MAP (Multiple Alignment Program), MBLKP, MBLKN, PIMA (Pattern-Induced Multi-sequence Alignment), SAGA (Sequence Alignment by Genetic Algorithm) and WHAT-IF. Such alignment programs can also be used to screen genome databases to identify polynucleotide sequences having substantially identical sequences.

A number of genome databases are available for comparison. Several databases containing genomic information annotated with some functional information are maintained by different organizations, and are accessible via the internet, for example, at world wide web addresses (url's) “wwwtigr.org/tdb”; “genetics.wisc.edu”; “genome-www.stanford.edu/˜ball”; “hiv-web.lanl.gov”; “ncbi.nlm.nih.gov”; “ebi.ac.uk”; “Pasteur.fr/other/biology”; and “genome.wi.mit.edu”.

In particular, the BLAST and BLAST 2.0 algorithms using default parameters are particularly useful for identifying polynucleotide and polypeptides encompassed within the present invention (Altschul et al. (Nucleic Acids Res. 25:3389-3402, 1977; J. Mol. Biol. 215:403-410, 1990, each of which is incorporated herein by reference). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra, 1977, 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectations (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci., USA 89:10915, 1989) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands.

The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, for example, Karlin and Altschul, Proc. Natl. Acad. Sci., USA 90:5873, 1993, which is incorporated herein by reference). One measure of similarity provided by BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a references sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001. Significantly, upon identifying polynucleotides that are substantially similar to those of SEQ ID NOS:1-5379, the identified polynucleotides can be used as query sequences in a BLAST search to identify polynucleotides and polypeptides substantially similar thereto.

It should be noted that the nucleotide sequences set forth as SEQ ID NOS:1-2703 comprise coding sequences, whereas the nucleotide sequences set forth as SEQ ID NOS:2704-5379 comprise regulatory sequences. In addition, the coding sequences and regulatory sequences are related in that, for example, SEQ ID NO:1 is the coding sequence of a plant cold regulated gene having a 5′ upstream (regulatory) sequence set forth as SEQ ID NO:2704 (see Table 2). Similarly, SEQ ID NO:2705 comprises a regulatory region of SEQ ID NO:2, SEQ ID NO:2706 comprises a regulatory region of SEQ ID NO:3, and so forth as shown in Table 2. As such, reference herein, for example, to a “polynucleotide comprising SEQ ID NO:1” can, unless indicated otherwise, include at least SEQ ID NO:2704. In some cases, the entire coding region of a plant stress regulated gene or the 5′ upstream sequence has not yet been determined (see, for example, SEQ ID NO:43 in Table 3, where “none” indicates that 5′ upstream regulatory sequences have not yet been determined). However, the determination of a complete coding sequence where only a portion is known or of regulatory sequences where a portion of the coding sequence is known can be made using methods as disclosed herein or otherwise known in the art.

In one embodiment, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool (“BLAST”). In particular, five specific BLAST programs are used to perform the following task:

(1) BLASTP and BLAST3 compare an amino acid query sequence against a protein sequence database;

(2) BLASTN compares a nucleotide query sequence against a nucleotide sequence database;

(3) BLASTX compares the six-frame conceptual translation products of a query nucleotide sequence (both strands) against a protein sequence database;

(4) TBLASTN compares a query protein sequence against a nucleotide sequence database translated in all six reading frames (both strands); and

(5) TBLASTX compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

The BLAST programs identify homologous sequences by identifying similar segments, which are referred to herein as “high-scoring segment pairs,” between a query amino or nucleic acid sequence and a test sequence which is preferably obtained from a protein or nucleic acid sequence database. High-scoring segment pairs are preferably identified (i.e., aligned) by means of a scoring matrix, many of which are known in the art. Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet et al., Science 256:1443-1445, 1992; Henikoff and Henikoff, Proteins 17:49-61, 1993, each of which is incorporated herein by reference). Less preferably, the PAM or PAM250 matrices may also be used (Schwartz and Dayhoff, eds., “Matrices for Detecting Distance Relationships: Atlas of Protein Sequence and Structure” (Washington, National Biomedical Research Foundation 1978)). BLAST programs are accessible through the U.S. National Library of Medicine, for example, on the world wide web at address (url) “ncbi.nlm.nih.gov”.

The parameters used with the above algorithms may be adapted depending on the sequence length and degree of homology studied. In some embodiments, the parameters may be the default parameters used by the algorithms in the absence of instructions from the user.

The term “substantially similar” also is used in reference to a comparison of expression profiles of nucleotide sequences, wherein a determination that an expression profile characteristic of a stress response is substantially similar to the profile of nucleic acid molecules expressed in a plant cell being examined (“test plant”) is indicative of exposure of the test plant cell to one or a combination of abiotic stress conditions. When used in reference to such a comparison of expression profiles, the term “substantially similar” means that that the individual nucleotide sequences in the test plant cell profile are altered in the same manner as the corresponding nucleotide sequences in the expression profile characteristic of the stress response.

By way of example, where exposure to saline results in an increased expression of nucleotide sequences A, B and C, and a decreased expression of nucleotide sequences D and E, as indicated by the expression profile characteristic of a saline stress response, a determination that corresponding nucleotide sequences A, B and C in the test plant cell are increased and that nucleotides sequences D and E are decreased is indicative of exposure of the test plant cell to a saline stress condition. It should be recognized that, where, for example, only nucleotide sequences A, B, D and E are examined in the test plant cell, an increase in A and B and a decrease in D and E expression of the test plant cells is considered to be substantially similar to the expression profile characteristic of a saline stress condition and, therefore, is indicative of exposure of the plant cell to a saline stress condition. Similarly, where the levels of expression of the nucleotide sequences examined in a test plant are altered in the same manner, i.e., are increased or are decreased, as that observed in an expression profile characteristic of a particular stress response, the absolute levels of expression may vary, for example, two-fold, five-fold, ten-fold, or the like. Nevertheless, the expression profile of the test plant cell is considered to be substantially similar to the expression profile characteristic of the particular stress response and, therefore, indicative of exposure of the plant cell to the stress condition.

As disclosed herein, clusters of stress-regulated genes (and their products), some of which also have been described as having cellular functions such as enzymatic activity or roles as transcription factors, are involved in the response of plant cells to various abiotic stresses (see Tables 29-31; see, also, Tables 1 and 32). As such, the polynucleotide sequences comprising the genes in a cluster likely share common stress-regulated regulatory elements, including, for example, cold-regulated regulatory elements (SEQ ID NOS:2704-3955), salinity-regulated regulatory elements (SEQ ID NOS:4910-5107, and osmotic pressure-regulated regulatory elements (SEQ ID NO:5108-5263), as well as regulatory elements that are responsive to a combination of stress conditions, but not to any of the individual stress conditions, alone (SEQ ID NOS:3956-4909 and 5263-5379). The identification of such clusters of genes thus provides a means to identify the stress-regulated regulatory elements that control the level of expression of these genes.

As used herein, the term “plant stress-regulated gene” means a polynucleotide sequence of a plant, the transcription of which is altered in response to exposure to a stress condition, and the regulatory elements linked to such a polynucleotide sequence and involved in the stress response, which can be induction or repression. In general, plant stress gene regulatory elements are contained within a sequence including approximately two kilobases upstream (5′) of the transcription or translation start site and two kilobases downstream (3′) of the transcription or translation termination site. In the absence of an abiotic stress condition, the stress-regulated gene can normally be unexpressed in the cells, can be expressed at a basal level, which is induced to a higher level in response to the stress condition, or can be expressed at a level that is reduced (decreased) in response to the stress condition. The coding region of a plant stress-regulated gene encodes a stress-regulated polypeptide, and also can be the basis for expression of a functional RNA molecule such as an antisense molecule or ribozyme. A stress-regulated polypeptide can have an adaptive effect on a plant, thereby allowing the plant to better tolerate stress conditions; or can have a maladaptive effect, thereby decreasing the ability of the plant to tolerate the stress conditions.

The present invention provides an isolated plant stress-regulated regulatory element, which regulates expression of an operatively linked nucleotide sequence in a plant in response a stress condition. As disclosed herein, a plant stress-regulated regulatory element can be isolated from a polynucleotide sequence of a plant stress-regulated gene comprising a nucleotide sequence as set forth in SEQ ID NOS:1-2703, for example any of SEQ ID NOS:2704-5379 (see Table 2). It is recognized that certain of the polynucleotides set forth as SEQ ID NOS:1-5379 previously have been described as being involved in a stress-regulated response in plants, including SEQ ID NOS:156, 229, 233, 558, 573, 606, 625, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918, and 1928 and, therefore, are not encompassed, in whole or in part, within the compositions of the invention, and are encompassed within only certain particular methods of the invention, for example, methods of making a transgenic plant that is resistant to two or more stress conditions, since, even where such a gene was known to be expressed in response to a single stress condition such as cold or saline (e.g., SEQ ID NO:1263), it was not known prior to the present disclosure that any of these genes was responsive to a combination of stress conditions (for example, a combination of cold and osmotic stress for SEQ ID NOS:1726, 1866, 1918, and 1928; or a combination of cold, osmotic and saline stress for SEQ ID NOS:1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, and 1634).

Methods for identifying and isolating the stress-regulated regulatory element from the disclosed polynucleotides, or genomic DNA clones corresponding thereto, are well known in the art. For example, methods of making deletion constructs or linker-scanner constructs can be used to identify nucleotide sequences that are responsive to a stress condition. Generally, such constructs include a reporter gene operatively linked to the sequence to be examined for regulatory activity. By performing such assays, a plant stress-regulated regulatory element can be defined within a sequence of about 500 nucleotides or fewer, generally at least about 200 nucleotides or fewer, particularly about 50 to 100 nucleotides, and more particularly at least about 20 nucleotides or fewer. Preferably the minimal (core) sequence required for regulating a stress response of a plant is identified.

The nucleotide sequences of the genes of a cluster also can be examined using a homology search engine such as described herein to identify sequences of conserved identity, particularly in the nucleotide sequence upstream of the transcription start site. Since all of the genes in a cluster as disclosed are induced in response to a particular stress condition or a particular combination of stress conditions, some or all of the nucleotide sequences can share conserved stress-regulated regulatory elements. By performing such a homology search, putative stress-regulated regulatory elements can be identified. The ability of such identified sequences to function as a plant stress-regulated regulatory element can be confirmed, for example, by operatively linking the sequence to a reporter gene and assaying the construct for responsiveness to a stress condition.

As used herein, the term “regulatory element” means a nucleotide sequence that, when operatively linked to a coding region of a gene, effects transcription of the coding region such that a ribonucleic acid (RNA) molecule is transcribed from the coding region. A regulatory element generally can increase or decrease the amount of transcription of a nucleotide sequence, for example, a coding sequence, operatively linked to the element with respect to the level at which the nucleotide sequence would be transcribed absent the regulatory element. Regulatory elements are well known in the art and include promoters, enhancers, silencers, inactivated silencer intron sequences, 3′-untranslated or 5′-untranslated sequences of transcribed sequence, for example, a poly-A signal sequence, or other protein or RNA stabilizing elements, or other gene expression control elements known to regulate gene expression or the amount of expression of a gene product. A regulatory element can be isolated from a naturally occurring genomic DNA sequence or can be synthetic, for example, a synthetic promoter.

Regulatory elements can be constitutively expressed regulatory element, which maintain gene expression at a relative level of activity (basal level), or can be regulated regulatory elements. Constitutively expressed regulatory elements can be expressed in any cell type, or can be tissue specific, which are expressed only in particular cell types, phase specific, which are expressed only during particular developmental or growth stages of a plant cell, or the like. A regulatory element such as a tissue specific or phase specific regulatory element or an inducible regulatory element useful in constructing a recombinant polynucleotide or in a practicing a method of the invention can be a regulatory element that generally, in nature, is found in a plant genome. However, the regulatory element also can be from an organism other than a plant, including, for example, from a plant virus, an animal virus, or a cell from an animal or other multicellular organism.

A regulatory element useful for practicing method of the present is a promoter element. Useful promoters include, but are not limited to, constitutive, inducible, temporally regulated, developmentally regulated, spatially-regulated, chemically regulated, stress-responsive, tissue-specific, viral and synthetic promoters. Promoter sequences are known to be strong or weak. A strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression. An inducible promoter is a promoter that provides for the turning on and off of gene expression in response to an exogenously added agent, or to an environmental or developmental stimulus. A bacterial promoter such as the P_(tac) promoter can be induced to varying levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed bacterial cells. An isolated promoter sequence that is a strong promoter for heterologous nucleic acid is advantageous because it provides for a sufficient level of gene expression to allow for easy detection and selection of transformed cells and provides for a high level of gene expression when desired.

Within a plant promoter region there are several domains that are necessary for full function of the promoter. The first of these domains lies immediately upstream of the structural gene and forms the “core promoter region” containing consensus sequences, normally 70 base pairs immediately upstream of the gene. The core promoter region contains the characteristic CAAT and TATA boxes plus surrounding sequences, and represents a transcription initiation sequence that defines the transcription start point for the structural gene.

The presence of the core promoter region defines a sequence as being a promoter: if the region is absent, the promoter is non-functional. The core promoter region, however, is insufficient to provide full promoter activity. A series of regulatory sequences upstream of the core constitute the remainder of the promoter. These regulatory sequences determine expression level, the spatial and temporal pattern of expression and, for an important subset of promoters, expression under inductive conditions (regulation by external factors such as light, temperature, chemicals, hormones).

To define a minimal promoter region, a DNA segment representing the promoter region is removed from the 5′ region of the gene of interest and operably linked to the coding sequence of a marker (reporter) gene by recombinant DNA techniques well known to the art. The reporter gene is operably linked downstream of the promoter, so that transcripts initiating at the promoter proceed through the reporter gene. Reporter genes generally encode proteins which are easily measured, including, but not limited to, chloramphenicol acetyl transferase (CAT), beta-glucuronidase (GUS), green fluorescent protein (GFP), é-galactosidase (é-GAL), and luciferase.

The construct containing the reporter gene under the control of the promoter is then introduced into an appropriate cell type by transfection techniques well known to the art. To assay for the reporter protein, cell lysates are prepared and appropriate assays, which are well known in the art, for the reporter protein are performed. For example, if CAT were the reporter gene of choice, the lysates from cells transfected with constructs containing CAT under the control of a promoter under study are mixed with isotopically labeled chloramphenicol and acetyl-coenzyme A (acetyl-CoA). The CAT enzyme transfers the acetyl group from acetyl-CoA to the 2-position or 3-position of chloramphenicol. The reaction is monitored by thin layer chromatography, which separates acetylated chloramphenicol from unreacted material. The reaction products are then visualized by autoradiography.

The level of enzyme activity corresponds to the amount of enzyme that was made, which in turn reveals the level of expression from the promoter of interest. This level of expression can be compared to other promoters to determine the relative strength of the promoter under study. In order to be sure that the level of expression is determined by the promoter, rather than by the stability of the mRNA, the level of the reporter mRNA can be measured directly, for example, by northern blot analysis.

Once activity is detected, mutational and/or deletional analyses may be employed to determine the minimal region and/or sequences required to initiate transcription. Thus, sequences can be deleted at the 5′ end of the promoter region and/or at the 3′ end of the promoter region, and nucleotide substitutions introduced. These constructs are then introduced to cells and their activity determined.

The choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the target species. In some cases, expression in multiple tissues is desirable. While in others, tissue-specific, e.g., leaf-specific, seed-specific, petal-specific, anther-specific, or pith-specific, expression is desirable. Although many promoters from dicotyledons have been shown to be operational in monocotyledons and vice versa, ideally dicotyledonous promoters are selected for expression in dicotyledons, and monocotyledonous promoters for expression in monocotyledons. There is, however, no restriction to the origin or source of a selected promoter. It is sufficient that the promoters are operational in driving the expression of a desired nucleotide sequence in the particular cell.

A range of naturally-occurring promoters are known to be operative in plants and have been used to drive the expression of heterologous (both foreign and endogenous) genes and nucleotide sequences in plants: for example, the constitutive 35S cauliflower mosaic virus (CaMV) promoter, the ripening-enhanced tomato polygalacturonase promoter (Bird et al., 1988), the E8 promoter (Diekman and Fischer, 1988) and the fruit specific 2A1 promoter (Pear et al., 1989). Many other promoters, e.g., U2 and U5 snRNA promoters from maize, the promoter from alcohol dehydrogenase, the Z4 promoter from a gene encoding the Z4 22 kD zein protein, the Z10 promoter from a gene encoding a 10 kD zein protein, a Z27 promoter from a gene encoding a 27 kD zein protein, the A20 promoter from the gene encoding a 19 kD zein protein, inducible promoters, such as the light inducible promoter derived from the pea rbcS gene and the actin promoter from rice, e.g., the actin 2 promoter (WO 00/70067); seed specific promoters, such as the phaseolin promoter from beans, may also be used. The nucleotide sequences of the stress-regulated genes of this invention can also be expressed under the regulation of promoters that are chemically regulated. This enables the nucleic acid sequence or encoded polypeptide to be synthesized only when the crop plants are treated with the inducing chemicals. Chemical induction of gene expression is detailed in EP 0 332 104 and U.S. Pat. No. 5,614,395.

In some instances it may be desirable to link a constitutive promoter to a polynucleotide comprising a stress regulated gene of the invention. Examples of some constitutive promoters include the rice actin 1 (Wang et al., 1992; U.S. Pat. No. 5,641,876), CaMV 35S (Odell et al., 1985), CaMV 19S (Lawton et al., 1987), nos, Adh, sucrose synthase; and the ubiquitin promoters.

In other situations it may be desirable to limit expression of stress-related sequences to specific tissues or stages of development. As used herein, the term “tissue specific or phase specific regulatory element” means a nucleotide sequence that effects transcription in only one or a few cell types, or only during one or a few stages of the life cycle of a plant, for example, only for a period of time during a particular stage of growth, development or differentiation. The terms “tissue specific” and “phase specific” are used together herein in referring to a regulatory element because a single regulatory element can have characteristics of both types of regulatory elements. For example, a regulatory element active only during a particular stage of plant development also can be expressed only in one or a few types of cells in the plant during the particular stage of development. As such, any attempt to classify such regulatory elements as tissue specific or as phase specific can be difficult. Accordingly, unless indicated otherwise, all regulatory elements having the characteristic of a tissue specific regulatory element, or a phase specific regulatory element, or both are considered together for purposes of the present invention.

Examples of tissue specific promoters which have been described include the lectin (Vodkin, 1983; Lindstrom et al., 1990) corn alcohol dehydrogenase 1 (Vogel et al., 1989; Dennis et al., 1984), corn light harvesting complex (Simpson, 1986; Bansal et al., 1992), corn heat shock protein (Odell et al., 1985), pea small subunit RuBP carboxylase (Poulsen et al., 1986), Ti plasmid mannopine synthase and Ti plasmid nopaline synthase (Langridge et al., 1989), petunia chalcone isomerase (vanTunen et al., 1988), bean glycine rich protein 1 (Keller et al., 1989), truncated CaMV 35S (Odell et al., 1985), potato patatin (Wenzler et al., 1989), root cell (Yamamoto et al., 1990), maize zein (Reina et al., 1990; Kriz et al., 1987; Wandelt et al., 1989; Langridge et al., 1983; Reina et al., 1990), globulin-1 (Belanger et al., 1991), α-tubulin, cab (Sullivan et al., 1989), PEPCase (Hudspeth & Grula, 1989), R gene complex-associated promoters (Chandler et al., 1989), histone, and chalcone synthase promoters (Franken et al., 1991). Tissue specific enhancers are described by Fromm et al. (1989).

Several other tissue-specific regulated genes and/or promoters have been reported in plants, including genes encoding seed storage proteins such as napin, cruciferin, beta-conglycinin, and phaseolin, zein or oil body proteins such as oleosin, genes involved in fatty acid biosynthesis, including acyl carrier protein, stearoyl-ACP desaturase, fatty acid desaturases (fad 2-1), and other genes expressed during embryonic development such as Bce4 (see, for example, EP 255378 and Kridl et al., 1991). Particularly useful for seed-specific expression is the pea vicilin promoter (Czako et al., 1992). (See also U.S. Pat. No. 5,625,136, which is incorporated herein by reference.) Other useful promoters for expression in mature leaves are those that are switched on at the onset of senescence, such as the SAG promoter from Arabidopsis (Gan et al., 1995).

A class of fruit-specific promoters expressed at or during antithesis through fruit development, at least until the beginning of ripening, is discussed in U.S. Pat. No. 4,943,674. cDNA clones that are preferentially expressed in cotton fiber have been isolated (John et al., 1992). cDNA clones from tomato displaying differential expression during fruit development have been isolated and characterized (Mansson et al., 1985, Slater et al., 1985). The promoter for polygalacturonase gene is active in fruit ripening. The polygalacturonase gene is described in U.S. Pat. Nos. 4,535,060, 4,769,061, 4,801,590, and 5,107,065, each of which is incorporated herein by reference.

Other examples of tissue-specific promoters include those that direct expression in leaf cells following damage to the leaf (for example, from chewing insects), in tubers (for example, patatin gene promoter), and in fiber cells (an example of a developmentally-regulated fiber cell protein is E6 (John et al., 1992). The E6 gene is most active in fiber, although low levels of transcripts are found in leaf, ovule and flower.

Additional tissue specific or phase specific regulatory elements include, for example, the AGL8/FRUITFULL regulatory element, which is activated upon floral induction (Hempel et al., Development 124:3845-3853, 1997, which is incorporated herein by reference); root specific regulatory elements such as the regulatory elements from the RCP1 gene and the LRP1 gene (Tsugeki and Fedoroff, Proc. Natl. Acad., USA 96:12941-12946, 1999; Smith and Fedoroff, Plant Cell 7:735-745, 1995, each of which is incorporated herein by reference); flower specific regulatory elements such as the regulatory elements from the LEAFY gene and the APETELA1 gene (Blazquez et al., Development 124:3835-3844, 1997, which is incorporated herein by reference; Hempel et al., supra, 1997); seed specific regulatory elements such as the regulatory element from the oleosin gene (Plant et al., Plant Mol. Biol. 25:193-205, 1994, which is incorporated herein by reference), and dehiscence zone specific regulatory element. Additional tissue specific or phase specific regulatory elements include the Zn13 promoter, which is a pollen specific promoter (Hamilton et al., Plant Mol. Biol. 18:211-218, 1992, which is incorporated herein by reference); the UNUSUAL FLORAL ORGANS (UFO) promoter, which is active in apical shoot meristem; the promoter active in shoot meristems (Atanassova et al., Plant J. 2:291, 1992, which is incorporated herein by reference), the cdc2a promoter and cyc07 promoter (see, for example, Ito et al., Plant Mol. Biol. 24:863, 1994; Martinez et al., Proc. Natl. Acad. Sci., USA 89:7360, 1992; Medford et al., Plant Cell 3:359, 1991; Terada et al., Plant J. 3:241, 1993; Wissenbach et al., Plant J. 4:411, 1993, each of which is incorporated herein by reference); the promoter of the APETELA3 gene, which is active in floral meristems (Jack et al., Cell 76:703, 1994, which is incorporated herein by reference; Hempel et al., supra, 1997); a promoter of an agamous-like (AGL) family member, for example, AGL8, which is active in shoot meristem upon the transition to flowering (Hempel et al., supra, 1997); floral abscission zone promoters; L1-specific promoters; and the like.

The tissue-specificity of some “tissue-specific” promoters may not be absolute and may be tested by one skilled in the art using the diphtheria toxin sequence. One can also achieve tissue-specific expression with “leaky” expression by a combination of different tissue-specific promoters (Beals et al., 1997). Other tissue-specific promoters can be isolated by one skilled in the art (see U.S. Pat. No. 5,589,379). Several inducible promoters (“gene switches”) have been reported, many of which are described in the review by Gatz (1996) and Gatz (1997). These include tetracycline repressor system, Lac repressor system, copper inducible systems, salicylate inducible systems (such as the PR1a system), glucocorticoid (Aoyama et al., 1997) and ecdysone inducible systems. Also included are the benzene sulphonamide (U.S. Pat. No. 5,364,780) and alcohol (WO 97/06269 and WO 97/06268) inducible systems and glutathione S-transferase promoters.

In some instances it might be desirable to inhibit expression of a native DNA sequence within a plant's tissues to achieve a desired phenotype. In this case, such inhibition might be accomplished with transformation of the plant to comprise a constitutive, tissue-independent promoter operably linked to an antisense nucleotide sequence, such that constitutive expression of the antisense sequence produces an RNA transcript that interferes with translation of the mRNA of the native DNA sequence.

Inducible regulatory elements also are useful for purposes of the present invention. As used herein, the term “inducible regulatory element” means a regulatory element that, when exposed to an inducing agent, effects an increased level of transcription of a nucleotide sequence to which it is operatively linked as compared to the level of transcription, if any, in the absence of an inducing agent. Inducible regulatory elements can be those that have no basal or constitutive activity and only effect transcription upon exposure to an inducing agent, or those that effect a basal or constitutive level of transcription, which is increased upon exposure to an inducing agent. Inducible regulatory elements that effect a basal or constitutive level of expression generally are useful in a method or composition of the invention where the induced level of transcription is substantially greater than the basal or constitutive level of expression, for example, at least about two-fold greater, or at least about five-fold greater. Particularly useful inducible regulatory elements do not have a basal or constitutive activity, or increase the level of transcription at least about ten-fold greater than a basal or constitutive level of transcription associated with the regulatory element.

Inducible promoters that have been described include the ABA- and turgor-inducible promoters, the promoter of the auxin-binding protein gene (Schwob et al., 1993), the UDP glucose flavonoid glycosyl-transferase gene promoter (Ralston et al., 1988), the MPI proteinase inhibitor promoter (Cordero et al., 1994), and the glyceraldehyde-3-phosphate dehydrogenase gene promoter (Kohler et al., 1995; Quigley et al., 1989; Martinez et al., 1989).

The term “inducing agent” is used to refer to a chemical, biological or physical agent or environmental condition that effects transcription from an inducible regulatory element. In response to exposure to an inducing agent, transcription from the inducible regulatory element generally is initiated de novo or is increased above a basal or constitutive level of expression. Such induction can be identified using the methods disclosed herein, including detecting an increased level of RNA transcribed from a nucleotide sequence operatively linked to the regulatory element, increased expression of a polypeptide encoded by the nucleotide sequence, or a phenotype conferred by expression of the encoded polypeptide.

An inducing agent useful in a method of the invention is selected based on the particular inducible regulatory element. For example, the inducible regulatory element can be a metallothionein regulatory element, a copper inducible regulatory element or a tetracycline inducible regulatory element, the transcription from which can be effected in response to metal ions, copper or tetracycline, respectively (Furst et al., Cell 55:705-717, 1988; Mett et al., Proc. Natl. Acad. Sci., USA 90:4567-4571, 1993; Gatz et al., Plant J. 2:397-404, 1992; Roder et al., Mol. Gen. Genet. 243:32-38, 1994, each of which is incorporated herein by reference). The inducible regulatory element also can be an ecdysone regulatory element or a glucocorticoid regulatory element, the transcription from which can be effected in response to ecdysone or other steroid (Christopherson et al., Proc. Natl. Acad. Sci., USA 89:6314-6318, 1992; Schena et al., Proc. Natl. Acad. Sci., USA 88:10421-10425, 1991, each of which is incorporated herein by reference). In addition, the regulatory element can be a cold responsive regulatory element or a heat shock regulatory element, the transcription of which can be effected in response to exposure to cold or heat, respectively (Takahashi et al., Plant Physiol. 99:383-390, 1992, which is incorporated herein by reference). Additional regulatory elements useful in the methods or compositions of the invention include, for example, the spinach nitrite reductase gene regulatory element (Back et al., Plant Mol. Biol. 17:9, 1991, which is incorporated herein by reference); a light inducible regulatory element (Feinbaum et al., Mol. Gen. Genet. 226:449, 1991; Lam and Chua, Science 248:471, 1990, each of which is incorporated herein by reference), a plant hormone inducible regulatory element (Yamaguchi-Shinozaki et al., Plant Mol. Biol. 15:905, 1990; Kares et al., Plant Mol. Biol. 15:225, 1990, each of which is incorporated herein by reference), and the like.

An inducible regulatory element also can be a plant stress-regulated regulatory element of the invention. In addition to the known stress conditions that specifically induce or repress expression from such elements, the present invention provides methods of identifying agents that mimic a stress condition. Accordingly, such stress mimics are considered inducing or repressing agents with respect to a plant stress-regulated regulatory element. In addition, a recombinant polypeptide comprising a zinc finger domain, which is specific for the regulatory element, and an effector domain, particularly an activator, can be useful as an inducing agent for a plant stress-regulated regulatory element. Furthermore, such a recombinant polypeptide provides the advantage that the effector domain can be a repressor domain, thereby providing a repressing agent, which decreases expression from the regulatory element. In addition, use of such a method of modulating expression of an endogenous plant stress-regulated gene provides the advantage that the polynucleotide encoding the recombinant polypeptide can be introduced into cells of the plant, thus providing a transgenic plant that can be regulated coordinately with the endogenous plant stress-regulated gene upon exposure to a stress condition. A polynucleotide encoding such a recombinant polypeptide can be operatively linked to and expressed from a constitutively active, inducible or tissue specific or phase specific regulatory element.

In one embodiment, the promoter may be a gamma zein promoter, an oleosin ole16 promoter, a globulin I promoter, an actin I promoter, an actin cl promoter, a sucrose synthetase promoter, an INOPS promoter, an EXM5 promoter, a globulin2 promoter, a b-32, ADPG-pyrophosphorylase promoter, an LtpI promoter, an Ltp2 promoter, an oleosin ole17 promoter, an oleosin ole18 promoter, an actin 2 promoter, a pollen-specific protein promoter, a pollen-specific pectate lyase promoter, an anther-specific protein promoter (Huffman), an anther-specific gene RTS2 promoter, a pollen-specific gene promoter, a tapeturn-specific gene promoter, tapeturn-specific gene RAB24 promoter, a anthranilate synthase alpha subunit promoter, an alpha zein promoter, an anthranilate synthase beta subunit promoter, a dihydrodipicolinate synthase promoter, a Thi 1 promoter, an alcohol dehydrogenase promoter, a cab binding protein promoter, an H3C4 promoter, a RUBISCO SS starch branching enzyme promoter, an ACCase promoter, an actin3 promoter, an actin7 promoter, a regulatory protein GF14-12 promoter, a ribosomal protein L9 promoter, a cellulose biosynthetic enzyme promoter, an S-adenosyl-L-homocysteine hydrolase promoter, a superoxide dismutase promoter, a C-kinase receptor promoter, a phosphoglycerate mutase promoter, a root-specific RCc3 mRNA promoter, a glucose-6 phosphate isomerase promoter, a pyrophosphate-fructose 6-phosphate-1-phosphotransferase promoter, an ubiquitin promoter, a beta-ketoacyl-ACP synthase promoter, a 33 kDa photosystem 11 promoter, an oxygen evolving protein promoter, a 69 kDa vacuolar ATPase subunit promoter, a metallothionein-like protein promoter, a glyceraldehyde-3-phosphate dehydrogenase promoter, an ABA- and ripening-inducible-like protein promoter, a phenylalanine ammonia lyase promoter, an adenosine triphosphatase S-adenosyl-L-homocysteine hydrolase promoter, an a-tubulin promoter, a cab promoter, a PEPCase promoter, an R gene promoter, a lectin promoter, a light harvesting complex promoter, a heat shock protein promoter, a chalcone synthase promoter, a zein promoter, a globulin-1 promoter, an ABA promoter, an auxin-binding protein promoter, a UDP glucose flavonoid glycosyl-transferase gene promoter, an NTI promoter, an actin promoter, an opaque 2 promoter, a b70 promoter, an oleosin promoter, a CaMV 35S promoter, a CaMV 19S promoter, a histone promoter, a turgor-inducible promoter, a pea small subunit RuBP carboxylase promoter, a Ti plasmid mannopine synthase promoter, Ti plasmid nopaline synthase promoter, a petunia chalcone isomerase promoter, a bean glycine rich protein I promoter, a CaMV 35S transcript promoter, a potato patatin promoter, or a S-E9 small subunit RuBP carboxylase promoter.

In addition to promoters, a variety of 5′ and 3′ transcriptional regulatory sequences are also available for use in the present invention. Transcriptional terminators are responsible for the termination of transcription and correct mRNA polyadenylation. The 3′-untranslated regulatory DNA sequence preferably includes from about 50 to about 1,000, more preferably about 100 to about 1,000, nucleotide base pairs and contains plant transcriptional and translational termination sequences. Appropriate transcriptional terminators and those which are known to function in plants include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator, the pea rbcS E9 terminator, the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3′ end of the protease inhibitor I or II genes from potato or tomato, although other 3′ elements known to those of skill in the art can also be employed. Alternatively, one also could use a gamma coixin, oleosin 3 or other terminator from the genus Coix. Preferred 3′ elements include those from the nopaline synthase gene of Agrobacterium tumefaciens (Bevan et al., 1983), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3′ end of the protease inhibitor I or II genes from potato or tomato.

As the DNA sequence between the transcription initiation site and the start of the coding sequence, i.e., the untranslated leader sequence, can influence gene expression, one may also wish to employ a particular leader sequence. Preferred leader sequences are contemplated to include those that include sequences predicted to direct optimum expression of the attached sequence, i.e., to include a preferred consensus leader sequence that may increase or maintain mRNA stability and prevent inappropriate initiation of translation. The choice of such sequences will be known to those of skill in the art in light of the present disclosure. Sequences that are derived from genes that are highly expressed in plants will be most preferred.

Other sequences that have been found to enhance gene expression in transgenic plants include intron sequences (e.g., from Adh1, bronze1, actin1, actin 2 (WO 00/760067), or the sucrose synthase intron) and viral leader sequences (e.g., from TMV, MCMV and AMV). For example, a number of non-translated leader sequences derived from viruses are known to enhance expression. Specifically, leader sequences from tobacco mosaic virus (TMV), maize chlorotic mottle virus (MCMV), and alfalfa mosaic virus (AMV) have been shown to be effective in enhancing expression (e.g., Gallie et al., 1987; Skuzeski et al., 1990). Other leaders known in the art include but are not limited to picornavirus leaders, for example, EMCV leader (encephalomyocarditis virus 5′ non-coding region; Elroy-Stein et al., 1989); potyvirus leaders, for example, TEV leader (tobacco etch virus); MDMV leader (maize dwarf mosaic virus); human immunoglobulin heavy chain binding protein (BiP) leader, (Macejak et al., 1991); untranslated leader from the coat protein mRNA of AMV (AMV RNA 4; Jobling et al., 1987), TMV (Gallie et al., 1989), and MCMV (Lommel et al., 1991; see also, della Cioppa et al., 1987).

Regulatory elements such as Adh intron 1 (Callis et al., 1987), sucrose synthase intron (Vasil et al., 1989) or TMV omega element (Gallie, et al., 1989), may further be included where desired. Examples of enhancers include elements from the CaMV 35S promoter, octopine synthase genes (Ellis et al., 1987), the rice actin I gene, the maize alcohol dehydrogenase gene (Callis et al., 1987), the maize shrunken I gene (Vasil et al., 1989), TMV Omega element (Gallie et al., 1989) and promoters from non-plant eukaryotes (e.g. yeast; Ma et al., 1988).

Vectors for use in accordance with the present invention may be constructed to include the ocs enhancer element, which was first identified as a 16 bp palindromic enhancer from the octopine synthase (ocs) gene of ultilane (Ellis et al., 1987), and is present in at least 10 other promoters (Bouchez et al., 1989). The use of an enhancer element, such as the ocs element and particularly multiple copies of the element, will act to increase the level of transcription from adjacent promoters when applied in the context of monocot transformation.

The methods of the invention provide genetically modified plant cells, which can contain, for example, a coding region, or peptide portion thereof, of a plant stress-regulated gene operatively linked to a heterologous inducible regulatory element; or a plant stress-regulated regulatory element operatively linked to a heterologous nucleotide sequence encoding a polypeptide of interest. In such a plant, the expression from the inducible regulatory element can be effected by exposing the plant cells to an inducing agent in any of numerous ways depending, for example, on the inducible regulatory element and the inducing agent. For example, where the inducible regulatory element is a cold responsive regulatory element present in the cells of a transgenic plant, the plant can be exposed to cold conditions, which can be produced artificially, for example, by placing the plant in a thermostatically controlled room, or naturally, for example, by planting the plant in an environment characterized, at least in part, by attaining temperatures sufficient to induce transcription from the promoter but not so cold as to kill the plants. By examining the phenotype of such transgenic plants, those plants that ectopically express a gene product that confers increased resistance of the plant to cold can be identified. Similarly, a transgenic plant containing a metallothionein promoter can be exposed to metal ions such as cadmium or copper by watering the plants with a solution containing the inducing metal ions, or can be planted in soil that is contaminated with a level of such metal ions that is toxic to most plants. The phenotype of surviving plants can be observed, those expressing desirable traits can be selected.

As used herein, the term “phenotype” refers to a physically detectable characteristic. A phenotype can be identified visually by inspecting the physical appearance of a plant following exposure, for example, to increased osmotic conditions; can be identified using an assay to detecting a product produced due to expression of reporter gene, for example, an RNA molecule, a polypeptide such as an enzyme, or other detectable signal such as disclosed herein; or by using any appropriate tool useful for identifying a phenotype of a plant, for example, a microscope, a fluorescence activated cell sorter, or the like.

A transgenic plant containing an inducible regulatory element such as a steroid inducible regulatory element can be exposed to a steroid by watering the plants with a solution containing the steroid. The use of an inducible regulatory element that is induced upon exposure to a chemical or biological inducing agent that can be placed in solution or suspension in an aqueous medium can be particularly useful because the inducing agent can be applied conveniently to a relatively large crop of transgenic plants containing the inducible regulatory element, for example, through a watering system or by spraying the inducing agent over the field. As such, inducible regulatory elements that are responsive to an environmental inducing agent, for example, cold; heat; metal ions or other potentially toxic agents such as a pesticides, which can contaminate a soil; or the like; or inducible regulatory elements that are regulated by inducing agents that conveniently can be applied to plants, can be particularly useful in a method or composition of the invention, and allow the identification and selection of plants that express desirable traits and survive and grow in environments that otherwise would not support growth of the plants.

As disclosed herein, the present invention provides plant stress-regulated regulatory elements, which are identified based on the expression of clusters of plant genes in response to stress. As used herein, the term “stress-regulated regulatory element of a plant” or “plant stress-regulated regulatory element” means a nucleotide sequence of a plant genome that can respond to a stress such that expression of a gene product encoded by a gene comprising the regulatory element (a stress-inducible gene) is increased above or decreased below the level of expression of the gene product in the absence of the stress condition. The regulatory element can be any gene regulatory element, including, for example, a promoter, an enhancer, a silencer, or the like. In one embodiment, the plant stress-regulated regulatory element is a plant stress-regulated promoter.

For purposes of modulating the responsiveness of a plant to a stress condition, it can be useful to introduce a modified plant stress-regulated regulatory element into a plant. Such a modified regulatory element can have any desirable characteristic, for example, it can be inducible to a greater level than the corresponding wild-type promoter, or it can be inactivated such that, upon exposure to a stress, there is little or no induction of expression of a nucleotide sequence operatively linked to the mutant element. A plant stress-regulated regulatory element can be modified by incorporating random mutations using, for example, in vitro recombination or DNA shuffling (Stemmer et al., Nature 370: 389-391, 1994; U.S. Pat. No. 5,605,793, each of which is incorporated herein by reference). Using such a method, millions of mutant copies of the polynucleotide, for example, stress-regulated regulatory element, can be produced based on the original nucleotide sequence, and variants with improved properties, such as increased inducibility can be recovered.

A mutation method such as DNA shuffling encompasses forming a mutagenized double-stranded polynucleotide from a template double-stranded polynucleotide, wherein the template double-stranded polynucleotide has been cleaved into double stranded random fragments of a desired size, and comprises the steps of adding to the resultant population of double-stranded random fragments one or more single or double stranded oligonucleotides, wherein the oligonucleotides comprise an area of identity and an area of heterology to the double stranded template polynucleotide; denaturing the resultant mixture of double stranded random fragments and oligonucleotides into single stranded fragments; incubating the resultant population of single stranded fragments with a polymerase under conditions that result in the annealing of the single stranded fragments at the areas of identity to form pairs of annealed fragments, the areas of identity being sufficient for one member of a pair to prime replication of the other, thereby forming a mutagenized double-stranded polynucleotide; and repeating the second and third steps for at least two further cycles, wherein the resultant mixture in the second step of a further cycle includes the mutagenized double-stranded polynucleotide from the third step of the previous cycle, and the further cycle forms a further mutagenized double-stranded polynucleotide. Preferably, the concentration of a single species of double stranded random fragment in the population of double stranded random fragments is less than 1% by weight of the total DNA. In addition, the template double stranded polynucleotide can comprise at least about 100 species of polynucleotides. The size of the double stranded random fragments can be from about 5 base pairs to 5 kilobase pairs. In a further embodiment, the fourth step of the method comprises repeating the second and the third steps for at least 10 cycles.

A plant stress-regulated regulatory element of the invention is useful for expressing a nucleotide sequence operatively linked to the element in a cell, particularly a plant cell. As used herein, the term “expression” refers to the transcription and/or translation of an endogenous gene or a transgene in plants. In the case of an antisense molecule, for example, the term “expression” refers to the transcription of the polynucleotide encoding the antisense molecule.

As used herein, the term “operatively linked,” when used in reference to a plant stress-regulated regulatory element, means that the regulatory element is positioned with respect to a second nucleotide sequence such that the regulatory element effects transcription or transcription and translation of the nucleotide sequence in substantially the same manner, but not necessarily to the same extent, as it does when the regulatory element is present in its natural position in a genome. Transcriptional promoters, for example, generally act in a position and orientation dependent manner and usually are positioned at or within about five nucleotides to about fifty nucleotides 5′ (upstream) of the start site of transcription of a gene in nature. In comparison, enhancers and silencers can act in a relatively position or orientation independent manner and, therefore, can be positioned several hundred or thousand nucleotides upstream or downstream from a transcription start site, or in an intron within the coding region of a gene, yet still be operatively linked to a coding region so as to effect transcription.

The second nucleotide sequence, i.e., the sequence operatively linked to the plant stress-regulated regulatory element, can be any nucleotide sequence, including, for example, a coding region of a gene or cDNA; a sequence encoding an antisense molecule, an RNAi molecule, ribozyme, triplexing agent (see, for example, Frank-Kamenetskii and Mirkin, Ann. Rev. Biochem. 64:65-95, 1995), or the like; or a sequence that, when transcribed, can be detected in the cell using, for example, by hybridization or amplification, or when translated produces a detectable signal. The term “coding region” is used broadly herein to include a nucleotide sequence of a genomic DNA or a cDNA molecule comprising all or part of a coding region of the coding strand. A coding region can be transcribed from an operatively linked regulatory element, and can be translated into a full length polypeptide or a peptide portion of a polypeptide. It should be recognized that, in a nucleotide sequence comprising a coding region, not all of the nucleotides in the sequence need necessarily encode the polypeptide and, particularly, that a gene transcript can contain one or more introns, which do not encode an amino acid sequence of a polypeptide but, nevertheless, are part of the coding region, particularly the coding strand, of the gene.

The present invention also relates to a recombinant polynucleotide, which contains a polynucleotide portion of a plant stress-regulated gene operatively linked to a heterologous nucleotide sequence. As used herein, the term “polynucleotide portion of plant stress-regulated sequence” means a contiguous nucleotide sequence of the plant stress-regulated gene that provides a function. The portion can be any portion of the sequence, particularly a coding sequence, or a sequence encoding a peptide portion of the stress-regulated polypeptide; the stress-regulated regulatory element; a sequence useful as an antisense molecule or triplexing agent; or a sequence useful for disrupting (knocking-out) an endogenous plant stress-regulated gene.

A heterologous nucleotide sequence is a nucleotide sequence that is not normally part of the plant stress-regulated gene from which the polynucleotide portion of the plant stress-regulated gene-component of the recombinant polynucleotide is obtained; or, if it is a part of the plant stress-regulated gene from which the polynucleotide portion is obtained, it is an orientation other than it would normally be in, for example, is an antisense sequence, or comprises at least partially discontinuous as compared to the genomic structure, for example, a single exon operatively linked to the regulatory element. In general, where the polynucleotide portion of the plant stress-regulated gene comprises the coding sequence in a recombinant polynucleotide of the invention, the heterologous nucleotide sequence will function as a regulatory element. The regulatory element can be any heterologous regulatory element, including, for example, a constitutively active regulatory element, an inducible regulatory element, or a tissue specific or phase specific regulatory element, as disclosed above. Conversely, where the polynucleotide portion of the plant stress-regulated polynucleotide comprises the stress-regulated regulatory element of a recombinant polynucleotide of the invention, the heterologous nucleotide sequence generally will be a nucleotide sequence that can be transcribed and, if desired, translated. Where the heterologous nucleotide sequence is expressed from a plant stress-regulated regulatory element, it generally confers a desirable phenotype to a plant cell containing the recombinant polynucleotide, or provides a means to identify a plant cell containing the recombinant polynucleotide. It should be recognized that a “desirable” phenotype can be one that decreases the ability of a plant cell to compete where the plant cell, or a plant containing the cell, is an undesired plant cell. Thus, a heterologous nucleotide sequence can allow a plant to grow, for example, under conditions in which it would not normally be able to grow.

A heterologous nucleotide sequence can be, or encode, a selectable marker. As used herein, the term “selectable marker” is used herein to refer to a molecule that, when present or expressed in a plant cell, provides a means to identify a plant cell containing the marker. As such, a selectable marker can provide a means for screening a population of plants, or plant cells, to identify those having the marker. A selectable marker also can confer a selective advantage to the plant cell, or a plant containing the cell. The selective advantage can be, for example, the ability to grow in the presence of a negative selective agent such as an antibiotic or herbicide, compared to the growth of plant cells that do not contain the selectable marker. The selective advantage also can be due, for example, to an enhanced or novel capacity to utilize an added compound as a nutrient, growth factor or energy source. A selectable advantage can be conferred, for example, by a single polynucleotide, or its expression product, or to a combination of polynucleotides whose expression in a plant cell gives the cell with a positive selective advantage, a negative selective advantage, or both.

Examples of selectable markers include those that confer antimetabolite resistance, for example, dihydrofolate reductase, which confers resistance to methotrexate (Reiss, Plant Physiol. (Life Sci. Adv.) 13:143-149, 1994); neomycin phosphotransferase, which confers resistance to the aminoglycosides neomycin, kanamycin and paromycin (Herrera-Estrella, EMBO J. 2:987-995, 1983) and hygro, which confers resistance to hygromycin (Marsh, Gene 32:481-485, 1984), trpB, which allows cells to utilize indole in place of tryptophan; hisD, which allows cells to utilize histinol in place of histidine (Hartman, Proc. Natl. Acad. Sci., USA 85:8047, 1988); mannose-6-phosphate isomerase which allows cells to utilize mannose (WO 94/20627); ornithine decarboxylase, which confers resistance to the ornithine decarboxylase inhibitor, 2-(difluoromethyl)-DL-ornithine (DFMO; McConlogue, 1987, In: Current Communications in Molecular Biology, Cold Spring Harbor Laboratory ed.); and deaminase from Aspergillus terreus, which confers resistance to Blasticidin S (Tamura, Biosci. Biotechnol. Biochem. 59:2336-2338, 1995). Additional selectable markers include those that confer herbicide resistance, for example, phosphinothricin acetyltransferase gene, which confers resistance to phosphinothricin (White et al., Nucl. Acids Res. 18:1062, 1990; Spencer et al., Theor. Appl. Genet. 79:625-631, 1990), a mutant EPSPV-synthase, which confers glyphosate resistance (Hinchee et al., Bio/Technology 91:915-922, 1998), a mutant acetolactate synthase, which confers imidazolione or sulfonylurea resistance (Lee et al., EMBO J. 7:1241-1248, 1988), a mutant psbA, which confers resistance to atrazine (Smeda et al., Plant Physiol. 103:911-917, 1993), or a mutant protoporphyrinogen oxidase (see U.S. Pat. No. 5,767,373), or other markers conferring resistance to an herbicide such as glufosinate. In addition, markers that facilitate identification of a plant cell containing the polynucleotide encoding the marker include, for example, luciferase (Giacomin, Plant Sci. 116:59-72, 1996; Scikantha, J. Bacteriol. 178:121, 1996), green fluorescent protein (Gerdes, FEBS Lett. 389:44-47, 1996) or f1-glucuronidase (Jefferson, EMBO J. 6:3901-3907, 1997), and numerous others as disclosed herein or otherwise known in the art. Such markers also can be used as reporter molecules.

A heterologous nucleotide sequence can encode an antisense molecule, particularly an antisense molecule specific for a nucleotide sequence of a plant stress-regulated gene, for example, the gene from which the regulatory component of the recombinant polynucleotide is derived. Such a recombinant polynucleotide can be useful for reducing the expression of a plant stress-regulated polypeptide in response to a stress condition because the antisense molecule, like the polypeptide, only will be induced upon exposure to the stress. A heterologous nucleotide sequence also can be, or can encode, a ribozyme or a triplexing agent. In addition to being useful as heterologous nucleotide sequences, such molecules also can be used directly in a method of the invention, for example, to modulate the responsiveness of a plant cell to a stress condition. Thus, an antisense molecule, ribozyme, or triplexing agent can be contacted directly with a target cell and, upon uptake by the cell, can effect their antisense, ribozyme or triplexing activity; or can be encoded by a heterologous nucleotide sequence that is expressed in a plant cell from a plant stress-regulated regulatory element, whereupon it can effect its activity.

An antisense polynucleotide, ribozyme or triplexing agent is complementary to a target sequence, which can be a DNA or RNA sequence, for example, messenger RNA, and can be a coding sequence, a nucleotide sequence comprising an intron-exon junction, a regulatory sequence such as a Shine-Delgarno-like sequence, or the like. The degree of complementarity is such that the polynucleotide, for example, an antisense polynucleotide, can interact specifically with the target sequence in a cell. Depending on the total length of the antisense or other polynucleotide, one or a few mismatches with respect to the target sequence can be tolerated without losing the specificity of the polynucleotide for its target sequence. Thus, few if any mismatches would be tolerated in an antisense molecule consisting, for example, of twenty nucleotides, whereas several mismatches will not affect the hybridization efficiency of an antisense molecule that is complementary, for example, to the full length of a target mRNA encoding a cellular polypeptide. The number of mismatches that can be tolerated can be estimated, for example, using well known formulas for determining hybridization kinetics (see Sambrook et al., “Molecular Cloning; A Laboratory Manual” 2nd Edition (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; 1989)) or can be determined empirically using methods as disclosed herein or otherwise known in the art, particularly by determining that the presence of the antisense polynucleotide, ribozyme, or triplexing agent in a cell decreases the level of the target sequence or the expression of a polypeptide encoded by the target sequence in the cell.

A nucleotide sequence useful as an antisense molecule, a ribozyme or a triplexing agent can inhibit translation or cleave a polynucleotide encoded by plant stress-regulated gene, thereby modulating the responsiveness of a plant cell to a stress condition. An antisense molecule, for example, can bind to an mRNA to form a double stranded molecule that cannot be translated in a cell. Antisense oligonucleotides of at least about 15 to 25 nucleotides are preferred since they are easily synthesized and can hybridize specifically with a target sequence, although longer antisense molecules can be expressed from a recombinant polynucleotide introduced into the target cell. Specific nucleotide sequences useful as antisense molecules can be identified using well known methods, for example, gene walking methods (see, for example, Seimiya et al., J. Biol. Chem. 272:4631-4636 (1997), which is incorporated herein by reference). Where the antisense molecule is contacted directly with a target cell, it can be operatively associated with a chemically reactive group such as iron-linked EDTA, which cleaves a target RNA at the site of hybridization. A triplexing agent, in comparison, can stall transcription (Maher et al., Antisense Res. Devel. 1:227 (1991); Helene, Anticancer Drug Design 6:569 (1991)).

A plant stress-regulated regulatory element can be included in an expression cassette. As used herein, the term “expression cassette” refers to a nucleotide sequence that can direct expression of an operatively linked polynucleotide. Thus, a plant stress-regulated regulatory element can constitute an expression cassette, or component thereof. An expression cassette is particularly useful for directing expression of a nucleotide sequence, which can be an endogenous nucleotide sequence or a heterologous nucleotide sequence, in a cell, particularly a plant cell. If desired, an expression cassette also can contain additional regulatory elements, for example, nucleotide sequences required for proper translation of a polynucleotide sequence into a polypeptide. In general, an expression cassette can be introduced into a plant cell such that the plant cell, a plant resulting from the plant cell, seeds obtained from such a plant, or plants produced from such seeds are resistant to a stress condition.

Additional regulatory sequences as disclosed above or other desirable sequences such as selectable markers or the like can be incorporated into an expression cassette containing a plant stress-regulated regulatory element (see, for example, WO 99/47552). Examples of suitable markers include dihydrofolate reductase (DHFR) or neomycin resistance for eukaryotic cells and tetracycline or ampicillin resistance for E. coli. Selection markers in plants include bleomycin, gentamycin, glyphosate, hygromycin, kanamycin, methotrexate, phleomycin, phosphinotricin, spectinomycin, streptomycin, sulfonamide and sulfonylureas resistance (see, for example, Maliga et al., Methods in Plant Molecular Biology, Cold Spring Harbor Laboratory Press, 1995, page 39). The selection marker can have its own promoter or its expression can be driven by the promoter operably linked to the sequence of interest. Additional sequences such as intron sequences (e.g. from Adh1 or bronze1) or viral leader sequences (e.g. from TMV, MCMV and AIVIV), all of which can enhance expression, can be included in the cassette. In addition, where it is desirable to target expression of a nucleotide sequence operatively linked to the stress-regulated regulatory element, a sequence encoding a cellular localization motif can be included in the cassette, for example, such that an encoded transcript or translation product is translocated to and localizes in the cytosol, nucleus, a chloroplast, or another subcellular organelle. Examples of useful transit peptides and transit peptide sequences can be found in Von Heijne et al., Plant Mol. Biol. Rep. 9: 104, 1991; Clark et al., J. Biol. Chem. 264:17544, 1989; della Cioppa et al., Plant Physiol. 84:965, 1987; Romer et al., Biochem. Biophys. Res. Comm. 196:1414, 1993; Shah et al., Science 233:478, 1986; Archer et al., J. Bioenerg Biomemb. 22:789, 1990; Scandalios, Prog. Clin. Biol. Res. 344:515, 1990; Weisbeek et al., J. Cell Sci. Suppl. 11:199, 1989; Bruce, Trends Cell Biol. 10:440, 2000. The present invention can utilize native or heterologous transit peptides. The encoding sequence for a transit peptide can include all or a portion of the encoding sequence for a particular transit peptide, and may also contain portions of the mature protein encoding sequence associated with a particular transit peptide.

A polynucleotide portion of a plant stress-regulated plant gene, or an expression cassette, can be introduced into a cell as a naked DNA molecule, can be incorporated in a matrix such as a liposome or a particle such as a viral particle, or can be incorporated into a vector. Such vectors can be cloning or expression vectors, but other uses are within the scope of the present invention. A cloning vector is a self-replicating DNA molecule that serves to transfer a DNA segment into a host cell. The three most common types of cloning vectors are bacterial plasmids, phages, and other viruses. An expression vector is a cloning vector designed so that a coding sequence inserted at a particular site will be transcribed and translated into a protein. Incorporation of the polynucleotide into a vector can facilitate manipulation of the polynucleotide, or introduction of the polynucleotide into a plant cell. A vector can be derived from a plasmid or a viral vector such as a T-DNA vector (Horsch et al., Science 227:1229-1231, 1985, which is incorporated herein by reference). If desired, the vector can comprise components of a plant transposable element, for example, a Ds transposon (Bancroft and Dean, Genetics 134:1221-1229, 1993, which is incorporated herein by reference) or an Spm transposon (Aarts et al., Mol. Gen. Genet. 247:555-564, 1995, which is incorporated herein by reference).

In addition to containing the polynucleotide portion of a plant stress-regulated gene, a vector can contain various nucleotide sequences that facilitate, for example, rescue of the vector from a transformed plant cell; passage of the vector in a host cell, which can be a plant, animal, bacterial, or insect host cell; or expression of an encoding nucleotide sequence in the vector, including all or a portion of a rescued coding region. As such, the vector can contain any of a number of additional transcription and translation elements, including constitutive and inducible promoters, enhancers, and the like (see, for example, Bitter et al., Meth. Enzymol. 153:516-544, 1987). For example, a vector can contain elements useful for passage, growth or expression in a bacterial system, including a bacterial origin of replication; a promoter, which can be an inducible promoter; and the like. In comparison, a vector that can be passaged in a mammalian host cell system can have a promoter such as a metallothionein promoter, which has characteristics of both a constitutive promoter and an inducible promoter, or a viral promoter such as a retrovirus long terminal repeat, an adenovirus late promoter, or the like. A vector also can contain one or more restriction endonuclease recognition and cleavage sites, including, for example, a polylinker sequence, to facilitate rescue of a nucleotide sequence operably linked to the polynucleotide portion.

The present invention also relates to a method of using a polynucleotide portion of a plant stress-regulated gene to confer a selective advantage on a plant cell. Such a method can be performed by introducing, for example, a plant stress-regulated regulatory element into a plant cell, wherein, upon exposure of the plant cell to a stress condition to which the regulatory element is responsive, a nucleotide sequence operatively linked to the regulatory element is expressed, thereby conferring a selective advantage to plant cell. The operatively linked nucleotide sequence can be a heterologous nucleotide sequence, which can be operatively linked to the regulatory element prior to introduction of the regulatory sequence into the plant cell; or can be an endogenous nucleotide sequence into which the regulatory element was targeted by a method such as homologous recombination. The selective advantage conferred by the operatively linked nucleotide sequence can be such that the plant is better able to tolerate the stress condition; or can be any other selective advantage.

As used herein, the term “selective advantage” refers to the ability of a particular organism to better propagate, develop, grow, survive, or otherwise tolerate a condition as compared to a corresponding reference organism that does not contain a plant-stress regulated polynucleotide portion of the present invention. In one embodiment, a selective advantage is exemplified by the ability of a desired plant, plant cell, or the like, that contains an introduced plant stress-regulated regulatory element, to grow better than an undesired plant, plant cell, or the like, that does not contain the introduced regulatory element. For example, a recombinant polynucleotide comprising a plant stress-regulated regulatory element operatively linked to a heterologous nucleotide sequence encoding an enzyme that inactivates an herbicide can be introduced in a desired plant. Upon exposure of a mixed population of plants comprising the desired plants, which contain the recombinant polynucleotide, and one or more other populations of undesired plants, which lack the recombinant polynucleotide, to a stress condition that induces expression of the regulatory element and to the herbicide, the desired plants will have a greater likelihood of surviving exposure to the toxin and, therefore, a selective advantage over the undesired plants.

In another embodiment, a selective advantage is exemplified by the ability of a desired plant, plant cell, or the like, to better propagate, develop, grow, survive, or otherwise tolerate a condition as compared to an undesired plant, plant cell, or the like, that contains an introduced plant stress-regulated regulatory element. For example, a recombinant polynucleotide comprising a plant stress-regulated regulatory element operatively linked to a plant cell toxin can be introduced into cells of an undesirable plant present in a mixed population of desired and undesired plants, for example, food crops and weeds, respectively, then the plants can be exposed to stress conditions that induce expression from the plant stress-regulated regulatory element, whereby expression of the plant cell toxin results in inhibition of growth or death of the undesired plants, thereby providing a selective advantage to the desired plants, which no longer have to compete with the undesired plants for nutrients, light, or the like. In another example, a plant stress-regulated regulatory element operatively linked to a plant cell toxin can be introduced into cells of plants used as a nurse crop. Nurse crops, also called cover or companion crops, are planted in combination with plants of interest to provide, among other things, shade and soil stability during establishment of the desired plants. Once the desired plants have become established, the presence of the nurse crop may no longer be desirable. Exposure to conditions inducing expression of the gene linked to the plant stress-regulated regulatory element allows elimination of the nurse crop. Alternatively nurse crops can be made less tolerate to abiotic stress by the inhibition of any of the stress-regulated sequences disclosed herein. Inhibition can be accomplished by any of the method described herein. Upon exposure of the nurse crop to the stress, the decreased ability of the nurse crop to respond to the stress will result in elimination of the nurse crop, leaving only the desired plants.

The invention also provides a means of producing a transgenic plant, which comprises plant cells that exhibit altered responsiveness to a stress condition. As such, the present invention further provides a transgenic plant, or plant cells or tissues derived therefrom, which are genetically modified to respond to stress differently than a corresponding wild-type plant or plant not containing constructs of the present invention would respond. As used herein, the term “responsiveness to a stress condition” refers to the ability of a plant to express a plant stress-regulated gene upon exposure to the stress condition. A transgenic plant cell contains a polypeptide portion of a plant stress-regulated gene, or a mutant form thereof, for example, a knock-out mutant. A knock-out mutant form of a plant stress-regulated gene can contain, for example, a mutation such that a STOP codon is introduced into the reading frame of the translated portion of the gene such that expression of a functional stress-regulated polypeptide is prevented; or a mutation in the stress-regulated regulatory element such that inducibility of the element in response to a stress condition is inhibited. Such transgenic plants of the invention can display any of various idiotypic modifications is response to an abiotic stress, including altered tolerance to the stress condition, as well as increased or decreased plant growth, root growth, yield, or the like, as compared to the corresponding wild-type plant.

The term “plant” is used broadly herein to include any plant at any stage of development, or to part of a plant, including a plant cutting, a plant cell, a plant cell culture, a plant organ, a plant seed, and a plantlet. A plant cell is the structural and physiological unit of the plant, comprising a protoplast and a cell wall. A plant cell can be in the form of an isolated single cell or a cultured cell, or can be part of higher organized unit, for example, a plant tissue, plant organ, or plant. Thus, a plant cell can be a protoplast, a gamete producing cell, or a cell or collection of cells that can regenerate into a whole plant. As such, a seed, which comprises multiple plant cells and is capable of regenerating into a whole plant, is considered plant cell for purposes of this disclosure. A plant tissue or plant organ can be a seed, protoplast, callus, or any other groups of plant cells that is organized into a structural or functional unit. Particularly useful parts of a plant include harvestable parts and parts useful for propagation of progeny plants. A harvestable part of a plant can be any useful part of a plant, for example, flowers, pollen, seedlings, tubers, leaves, stems, fruit, seeds, roots, and the like. A part of a plant useful for propagation includes, for example, seeds, fruits, cuttings, seedlings, tubers, rootstocks, and the like.

A transgenic plant can be regenerated from a transformed plant cell. As used herein, the term “regenerate” means growing a whole plant from a plant cell; a group of plant cells; a protoplast; a seed; or a piece of a plant such as a callus or tissue. Regeneration from protoplasts varies from species to species of plants. For example, a suspension of protoplasts can be made and, in certain species, embryo formation can be induced from the protoplast suspension, to the stage of ripening and germination. The culture media generally contains various components necessary for growth and regeneration, including, for example, hormones such as auxins and cytokinins; and amino acids such as glutamic acid and proline, depending on the particular plant species. Efficient regeneration will depend, in part, on the medium, the genotype, and the history of the culture. If these variables are controlled, however, regeneration is reproducible.

Regeneration can occur from plant callus, explants, organs or plant parts. Transformation can be performed in the context of organ or plant part regeneration. (see Meth. Enzymol. Vol. 118; Klee et al. Ann. Rev. Plant Physiol. 38:467, 1987, which is incorporated herein by reference). Utilizing the leaf disk-transformation-regeneration method, for example, disks are cultured on selective media, followed by shoot formation in about two to four weeks (see Horsch et al., supra, 1985). Shoots that develop are excised from calli and transplanted to appropriate root-inducing selective medium. Rooted plantlets are transplanted to soil as soon as possible after roots appear. The plantlets can be repotted as required, until reaching maturity.

In vegetatively propagated crops, the mature transgenic plants are propagated utilizing cuttings or tissue culture techniques to produce multiple identical plants. Selection of desirable transgenotes is made and new varieties are obtained and propagated vegetatively for commercial use. In seed propagated crops, the mature transgenic plants can be self crossed to produce a homozygous inbred plant. The resulting inbred plant produces seeds that contain the introduced plant stress-induced regulatory element, and can be grown to produce plants that express a polynucleotide or polypeptide in response to a stress condition that induces expression from the regulatory element. As such, the invention further provides seeds produced by a transgenic plant obtained by a method of the invention.

In addition, transgenic plants comprising different recombinant sequences can be crossbred, thereby providing a means to obtain transgenic plants containing two or more different transgenes, each of which contributes a desirable characteristic to the plant. Methods for breeding plants and selecting for crossbred plants having desirable characteristics or other characteristics of interest are well known in the art.

A method of the invention can be performed by introducing a polynucleotide portion of a plant stress-regulated gene into the plant. As used herein, the term “introducing” means transferring a polynucleotide into a plant cell. A polynucleotide can be introduced into a cell by a variety of methods well known to those of ordinary skill in the art. For example, the polynucleotide can be introduced-into a plant cell using a direct gene transfer method such as electroporation or microprojectile mediated transformation, or using Agrobacterium mediated transformation. Non-limiting examples of methods for the introduction of polynucleotides into plants are provided in greater detail herein. As used herein, the term “transformed” refers to a plant cell containing an exogenously introduced polynucleotide portion of a plant stress-regulated gene that is or can be rendered active in a plant cell, or to a plant comprising a plant cell containing such a polynucleotide.

It should be recognized that one or more polynucleotides, which are the same or different can be introduced into a plant, thereby providing a means to obtain a genetically modified plant containing multiple copies of a single transgenic sequence, or containing two or more different transgenic sequences, either or both of which can be present in multiple copies. Such transgenic plants can be produced, for example, by simply selecting plants having multiple copies of a single type of transgenic sequence; by cotransfecting plant cells with two or more populations of different transgenic sequences and identifying those containing the two or more different transgenic sequences; or by crossbreeding transgenic plants, each of which contains one or more desired transgenic sequences, and identifying those progeny having the desired sequences.

Methods for introducing a polynucleotide into a plant cell to obtain a transformed plant also include direct gene transfer (see European Patent A 164 575), injection, electroporation, biolistic methods such as particle bombardment, pollen-mediated transformation, plant RNA virus-mediated transformation, liposome-mediated transformation, transformation using wounded or enzyme-degraded immature embryos, or wounded or enzyme-degraded embryogenic callus, and the like. Transformation methods using Agrobacterium tumefaciens tumor inducing (Ti) plasm ids or root-inducing (R1) plasmids, or plant virus vectors are well known in the art (see, for example, WO 99/47552; Weissbach & Weissbach, “Methods for Plant Molecular Biology” (Academic Press, NY 1988), section VIII, pages 421-463; Grierson and Corey, “Plant Molecular Biology” 2d Ed. (Blackie, London 1988), Chapters 7-9, each of which is incorporated herein by reference; Horsch et al., supra, 1985). The wild-type form of Agrobacterium, for example, contains a Ti plasmid, which directs production of tumorigenic crown gall growth on host plants. Transfer of the tumor inducing T-DNA region of the Ti plasmid to a plant genome requires the Ti plasmid-encoded virulence genes as well as T-DNA borders, which are a set of direct DNA repeats that delineate the region to be transferred. An Agrobacterium based vector is a modified form of a Ti plasmid, in which the tumor inducing functions are replaced by a nucleotide sequence of interest that is to be introduced into the plant host.

Methods of using Agrobacterium mediated transformation include cocultivation of Agrobacterium with cultured isolated protoplasts; transformation of plant cells or tissues with Agrobacterium; and transformation of seeds, apices or meristems with Agrobacterium. In addition, in planta transformation by Agrobacterium can be performed using vacuum infiltration of a suspension of Agrobacterium cells (Bechtold et al., C.R. Acad. Sci. Paris 316:1194, 1993, which is incorporated herein by reference).

Agrobacterium mediated transformation can employ cointegrate vectors or binary vector systems, in which the components of the Ti plasmid are divided between a helper vector, which resides permanently in the Agrobacterium host and carries the virulence genes, and a shuttle vector, which contains the gene of interest bounded by T-DNA sequences. Binary vectors are well known in the art (see, for example, De Framond, BioTechnology 1:262, 1983; Hoekema et al., Nature 303:179, 1983, each of which is incorporated herein by reference) and are commercially available (Clontech; Palo Alto Calif.). For transformation, Agrobacterium can be cocultured, for example, with plant cells or wounded tissue such as leaf tissue, root explants, hypocotyledons, stem pieces or tubers (see, for example, Glick and Thompson, “Methods in Plant Molecular Biology and Biotechnology” (Boca Raton Fla., CRC Press 1993), which is incorporated herein by reference). Wounded cells within the plant tissue that have been infected by Agrobacterium can develop organs de novo when cultured under the appropriate conditions; the resulting transgenic shoots eventually give rise to transgenic plants, which contain an exogenous polynucleotide portion of a plant stress-regulated gene.

Agrobacterium mediated transformation has been used to produce a variety of transgenic plants, including, for example, transgenic cruciferous plants such as Arabidopsis, mustard, rapeseed and flax; transgenic leguminous plants such as alfalfa, pea, soybean, trefoil and white clover; and transgenic solanaceous plants such as eggplant, petunia, potato, tobacco and tomato (see, for example, Wang et al., “Transformation of Plants and Soil Microorganisms” (Cambridge, University Press 1995), which is incorporated herein by reference). In addition, Agrobacterium mediated transformation can be used to introduce an exogenous polynucleotide sequence, for example, a plant stress-regulated regulatory element into apple, aspen, belladonna, black currant, carrot, celery, cotton, cucumber, grape, horseradish, lettuce, morning glory, muskmelon, neem, poplar, strawberry, sugar beet, sunflower, walnut, asparagus, rice and other plants (see, for example, Glick and Thompson, supra, 1993; Hiei et al., Plant J. 6:271-282, 1994; Shimamoto, Science 270:1772-1773, 1995).

Suitable strains of Agrobacterium tumefaciens and vectors as well as transformation of Agrobacteria and appropriate growth and selection media are well known in the art (GV3101, pMK90RK), Koncz, Mol. Gen. Genet. 204:383-396, 1986; (C58C1, pGV3850kan), Deblaere, Nucl. Acid Res. 13:4777, 1985; Bevan, Nucl. Acid Res. 12:8711, 1984; Koncz, Proc. Natl. Acad. Sci. USA 86:8467-8471, 1986; Koncz, Plant Mol. Biol. 20:963-976, 1992; Koncz, Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual Vol. 2, Gelvin and Schilperoort (Eds.), Dordrecht, The Netherlands: Kluwer Academic Publ. (1994), 1-22; European Patent A-1 20 516; Hoekema: The Binary Plant Vector System, Offsetdrukkerij Kanters B. V., Alblasserdam (1985), Chapter V; Fraley, Crit. Rev. Plant. Sci., 4:1-46; An, EMBO J. 4:277-287, 1985).

Where a polynucleotide portion of a plant stress-regulated gene is contained in vector, the vector can contain functional elements, for example “left border” and “right border” sequences of the T-DNA of Agrobacterium, which allow for stable integration into a plant genome. Furthermore, methods and vectors that permit the generation of marker-free transgenic plants, for example, where a selectable marker gene is lost at a certain stage of plant development or plant breeding, are known, and include, for example, methods of co-transformation (Lyznik, Plant Mol. Biol. 13:151-161, 1989; Peng, Plant Mol. Biol. 27:91-104, 1995), or methods that utilize enzymes capable of promoting homologous recombination in plants (see, e.g., WO97/08331; Bayley, Plant Mol. Biol. 18:353-361, 1992; Lloyd, Mol. Gen. Genet. 242:653-657, 1994; Maeser, Mol. Gen. Genet. 230:170-176, 1991; Onouchi, Nucl. Acids Res. 19:6373-6378, 1991; see, also, Sambrook et al., supra, 1989).

A direct gene transfer method such as electroporation also can be used to introduce a polynucleotide portion of a plant stress-regulated gene into a cell such as a plant cell. For example, plant protoplasts can be electroporated in the presence of the regulatory element, which can be in a vector (Fromm et al., Proc. Natl. Acad. Sci., USA 82:5824, 1985, which is incorporated herein by reference). Electrical impulses of high field strength reversibly permeabilize membranes allowing the introduction of the nucleic acid. Electroporated plant protoplasts reform the cell wall, divide and form a plant callus. Microinjection can be performed as described in Potrykus and Spangenberg (eds.), Gene Transfer To Plants (Springer Verlag, Berlin, N.Y. 1995). A transformed plant cell containing the introduced polynucleotide can be identified by detecting a phenotype due to the introduced polynucleotide, for example, increased or decreased tolerance to a stress condition.

Microprojectile mediated transformation also can be used to introduce a polynucleotide into a plant cell (Klein et al., Nature 327:70-73, 1987, which is incorporated herein by reference). This method utilizes microprojectiles such as gold or tungsten, which are coated with the desired nucleic acid molecule by precipitation with calcium chloride, spermidine or polyethylene glycol. The microprojectile particles are accelerated at high speed into a plant tissue using a device such as the BIOLISTIC PD-1000 (BioRad; Hercules Calif.).

Microprojectile mediated delivery (“particle bombardment”) is especially useful to transform plant cells that are difficult to transform or regenerate using other methods. Methods for the transformation using biolistic methods are well known (Wan, Plant Physiol. 104:37-48, 1984; Vasil, Bio/Technology 11:1553-1558, 1993; Christou, Trends in Plant Science 1:423-431, 1996). Microprojectile mediated transformation has been used, for example, to generate a variety of transgenic plant species, including cotton, tobacco, corn, hybrid poplar and papaya (see Glick and Thompson, supra, 1993). Important cereal crops such as wheat, oat, barley, sorghum and rice also have been transformed using microprojectile mediated delivery (Duan et al., Nature Biotech. 14:494-498, 1996; Shimamoto, Curr. Opin. Biotech. 5:158-162, 1994). A rapid transformation regeneration system for the production of transgenic plants such as a system that produces transgenic wheat in two to three months (see European Patent No. EP 0709462A2, which is incorporated herein by reference) also can be useful for producing a transgenic plant using a method of the invention, thus allowing more rapid identification of gene functions. The transformation of most dicotyledonous plants is possible with the methods described above. Transformation of monocotyledonous plants also can be transformed using, for example, biolistic methods as described above, protoplast transformation, electroporation of partially permeabilized cells, introduction of DNA using glass fibers, Agrobacterium mediated transformation, and the like.

Plastid transformation also can be used to introduce a polynucleotide portion of a plant stress-regulated gene into a plant cell (U.S. Pat. Nos. 5,451,513, 5,545,817, and 5,545,818; WO 95/16783; McBride et al., Proc. Natl. Acad. Sci., USA 91:7301-7305, 1994). Chloroplast transformation involves introducing regions of cloned plastid DNA flanking a desired nucleotide sequence, for example, a selectable marker together with polynucleotide of interest into a suitable target tissue, using, for example, a biolistic or protoplast transformation method (e.g., calcium chloride or PEG mediated transformation). One to 1.5 kb flanking regions (“targeting sequences”) facilitate homologous recombination with the plastid genome, and allow the replacement or modification of specific regions of the plastome. Using this method, point mutations in the chloroplast 16S rRNA and rps12 genes, which confer resistance to spectinomycin and streptomycin, can be utilized as selectable markers for transformation (Svab et al., Proc. Natl. Acad. Sci., USA 87:8526-8530, 1990; Staub and Maliga, Plant Cell 4:39-45, 1992), resulted in stable homopiasmic transformants; at a frequency of approximately one per 100 bombardments of target leaves. The presence of cloning sites between these markers allowed creation of a plastid targeting vector for introduction of foreign genes (Staub and Maliga, EMBO J. 12:601-606, 1993). Substantial increases in transformation frequency are obtained by replacement of the recessive rRNA or r-protein antibiotic resistance genes with a dominant selectable marker, the bacterial aadA gene encoding the spectinomycin-detoxifying enzyme aminoglycoside-3′-adenyltransf erase (Svab and Maliga, Proc. Natl. Acad. Sci., USA 90:913-917, 1993). Approximately 15 to 20 cell division cycles following transformation are generally required to reach a homoplastidic state. Plastid expression, in which genes are inserted by homologous recombination into all of the several thousand copies of the circular plastid genome present in each plant cell, takes advantage of the enormous copy number advantage over nuclear-expressed genes to permit expression levels that can readily exceed 10% of the total soluble plant protein.

Plants suitable to treatment according to a method of the invention can be monocots or dicots and include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassaya (Manihot esculenta), coffee (Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea ultilane), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, duckweed (Lemna), barley, tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).

Ornamentals such as azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum are also included. Additional ornamentals within the scope of the invention include impatiens, Begonia, Pelargonium, Viola, Cyclamen, Verbena, Vinca, Tagetes, Primula, Saint Paulia, Agertum, Amaranthus, Antihirrhinum, Aquilegia, Cineraria, Clover, Cosmo, Cowpea, Dahlia, Datura, Delphinium, Gerbera, Gladiolus, Gloxinia, Hippeastrum, Mesembryanthemum, Salpiglossos, and Zinnia.

Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga ultilane); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis).

Leguminous plants which may be used in the practice of the present invention include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc. Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo. Preferred forage and turf grass for use in the methods of the invention include alfalfa, orchard grass, tall fescue, perennial ryegrass, creeping bent grass, and redtop.

Other plants within the scope of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, ultilan sprouts, onion, carrot, leek, beet, broad bean, celery, radish, pumpkin, endive, gourd, garlic, snapbean, spinach, squash, turnip, ultilane, chicory, groundnut and zucchini.

Angiosperms are divided into two broad classes based on the number of cotyledons, which are seed leaves that generally store or absorb food; a monocotyledonous angiosperm has a single cotyledon, and a dicotyledonous angiosperm has two cotyledons. Angiosperms produce a variety of useful products including materials such as lumber, rubber, and paper; fibers such as cotton and linen; herbs and medicines such as quinine and vinblastine; ornamental flowers such as roses and orchids; and foodstuffs such as grains, oils, fruits and vegetables.

Angiosperms encompass a variety of flowering plants, including, for example, cereal plants, leguminous plants, oilseed plants, hardwood trees, fruit-bearing plants and ornamental flowers, which general classes are not necessarily exclusive. Cereal plants, which produce an edible grain cereal, include, for example, corn, rice, wheat, barley, oat, rye, orchardgrass, guinea grass, sorghum and turfgrass. Leguminous plants include members of the pea family (Fabaceae) and produce a characteristic fruit known as a legume. Examples of leguminous plants include, for example, soybean, pea, chickpea, moth bean, broad bean, kidney bean, lima bean, lentil, cowpea, dry bean, and peanut, as well as alfalfa, birdsfoot trefoil, clover and sainfoin. Oilseed plants, which have seeds that are useful as a source of oil, include soybean, sunflower, rapeseed (canola) and cottonseed.

Angiosperms also include hardwood trees, which are perennial woody plants that generally have a single stem (trunk). Examples of such trees include alder, ash, aspen, basswood (linden), beech, birch, cherry, cottonwood, elm, eucalyptus, hickory, locust, maple, oak, persimmon, poplar, sycamore, walnut, sequoia, and willow. Trees are useful, for example, as a source of pulp, paper, structural material and fuel.

Angiosperms are fruit-bearing plants that produce a mature, ripened ovary, which generally contains seeds. A fruit can be suitable for human or animal consumption or for collection of seeds to propagate the species. For example, hops are a member of the mulberry family that are prized for their flavoring in malt liquor. Fruit-bearing angiosperms also include grape, orange, lemon, grapefruit, avocado, date, peach, cherry, olive, plum, coconut, apple and pear trees and blackberry, blueberry, raspberry, strawberry, pineapple, tomato, cucumber and eggplant plants. An ornamental flower is an angiosperm cultivated for its decorative flower. Examples of commercially important ornamental flowers include rose, orchid, lily, tulip and chrysanthemum, snapdragon, camellia, carnation and petunia plants. The skilled artisan will recognize that the methods of the invention can be practiced using these or other angiosperms, as desired, as well as gymnosperms, which do not produce seeds in a fruit.

A method of producing a transgenic plant can be performed by introducing a polynucleotide portion of plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cell to a stress condition, thereby producing a transgenic plant, which comprises plant cells that exhibit altered responsiveness to the stress condition. In one embodiment, the polynucleotide portion of the plant stress-regulated gene encodes a stress-regulated polypeptide or functional peptide portion thereof, wherein expression of the stress-regulated polypeptide or functional peptide portion thereof either increases the stress tolerance of the transgenic plant, or decreases the stress tolerance of the transgenic plant. The polynucleotide portion of the plant stress-regulated gene encoding the stress-regulated polypeptide or functional peptide portion thereof can be operatively linked to a heterologous promoter.

In another embodiment, the polynucleotide portion of the plant stress-regulated gene comprises a stress-regulated regulatory element. The stress-regulated regulatory element can integrate into the plant cell genome in a site-specific manner, whereupon it can be operatively linked to an endogenous nucleotide sequence, which can be expressed in response to a stress condition specific for the regulatory element; or can be a mutant regulatory element, which is not responsive to the stress condition, whereby upon integrating into the plant cell genome, the mutant regulatory element disrupts an endogenous stress-regulated regulatory element of a plant stress-regulated gene, thereby altering the responsiveness of the plant stress-regulated gene to the stress condition. Accordingly, the invention also provides genetically modified plants, including transgenic plants, produced by such a method, and a plant cell obtained from such genetically modified plant, wherein said plant cell exhibits altered responsiveness to the stress condition; a seed produced by a transgenic plant; and a cDNA library prepared from a transgenic plant.

Also provided is a method of modulating the responsiveness of a plant cell to a stress condition. Such a method can be performed, for example, by introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, thereby modulating the responsiveness of the plant cell to a stress condition. As disclosed herein, the responsiveness of the plant cell can be increased or decreased upon exposure to the stress condition, and the altered responsiveness can result in increased or decreased tolerance of the plant cell to a stress condition. The polynucleotide portion of the plant stress-regulated gene can, but need not, be integrated into the genome of the plant cell, thereby modulating the responsiveness of the plant cell to the stress condition. Accordingly, the invention also provide a genetically modified plant, including a transgenic plant, which contains an introduced polynucleotide portion of a plant stress-regulated gene, as well as plant cells, tissues, and the like, which exhibit modulated responsiveness to a stress condition.

The polynucleotide portion of the plant stress-regulated gene can encode a stress-regulated polypeptide or functional peptide portion thereof, which can be operatively linked to a heterologous promoter. As used herein, reference to a “functional peptide portion of a plant stress-regulated polypeptide” means a contiguous amino acid sequence of the polypeptide that has an activity of the full length polypeptide, or that has an antagonist activity with respect to the full length polypeptide, or that presents an epitope unique to the polypeptide. Thus, by expressing a functional peptide portion of a plant stress-regulated polypeptide in a plant cell, the peptide can act as an agonist or an antagonist of the polypeptide, thereby modulating the responsiveness of the plant cell to a stress condition.

A polynucleotide portion of the plant stress-regulated nucleotide sequence also can contain a mutation, whereby upon integrating into the plant cell genome, the polynucleotide disrupts (knocks-out) an endogenous plant stress-regulated nucleotide sequence, thereby modulating the responsiveness of said plant cell to the stress condition. Depending on whether the knocked-out gene encodes an adaptive or a maladaptive stress-regulated polypeptide, the responsiveness of the plant will be modulated accordingly. Thus, a method of the invention provides a means of producing a transgenic plant having a knock-out phenotype of a plant stress-regulated nucleotide sequence.

Alternatively, the responsiveness of a plant or plant cell to a stress condition can be modulated by use of a suppressor construct containing dominant negative mutation for any of the stress-regulated sequences described herein. Expression of a suppressor construct containing a dominant mutant mutation generates a mutant transcript that, when coexpressed with the wild-type transcript inhibits the action of the wild-type transcript. Methods for the design and use of dominant negative constructs are well known (see, for example, in Herskowitz, Nature 329:219-222, 1987; Lagna and Hemmati-Brivanlou, Curr. Topics Devel. Biol. 36:75-98, 1998).

The polynucleotide portion of the plant stress-regulated gene also can comprise a stress-regulated regulatory element, which can be operatively linked to a heterologous nucleotide sequence, which, upon expression from the regulatory element in response to a stress condition, modulates the responsiveness of the plant cell to the stress condition. Such a heterologous nucleotide sequence can encode, for example, a stress-inducible transcription factor such as DREB1A, which, upon exposure to the stress condition, is expressed such that it can amplify the stress response (see Kasuga et al., supra, 1999). The heterologous nucleotide sequence also can encode a polynucleotide that is specific for a plant stress-regulated gene, for example, an antisense molecule, a ribozyme, and a triplexing agent, either of which, upon expression in the plant cell, reduces or inhibits expression of a stress-regulated polypeptide encoded by the gene, thereby modulating the responsiveness of the plant cell to a stress condition, for example, an abnormal level of cold, osmotic pressure, and salinity. As used herein, the term “abnormal,” when used in reference to a condition such as temperature, osmotic pressure, salinity, or any other condition that can be a stress condition, means that the condition varies sufficiently from a range generally considered optimum for growth of a plant that the condition results in an induction of a stress response in a plant. Methods of determining whether a stress response has been induced in a plant are disclosed herein or otherwise known in the art.

A plant stress-regulated regulatory element can be operatively linked to a heterologous polynucleotide sequence, such that the regulatory element can be introduced into a plant genome in a site-specific matter by homologous recombination. For example, a mutant plant stress-regulated regulatory element for a maladaptive stress-induced polypeptide can be transformed into a plant genome in a site specific manner by in vivo mutagenesis, using a hybrid RNA-DNA oligonucleotide (“chimeroplast” (TIBTECH 15:441-447, 1997; WO 95/15972; Kren, Hepatology 25:1462-1468, 1997; Cole-Strauss, Science 273:1386-1389, 1996, each of which is incorporated herein by reference). Part of the DNA component of the RNA-DNA oligonucleotide is homologous to a nucleotide sequence comprising the regulatory element of the maladaptive gene, but includes a mutation or contains a heterologous region which is surrounded by the homologous regions. By means of base pairing of the homologous regions of the RNA-DNA oligonucleotide and of the endogenous nucleic acid molecule, followed by a homologous recombination the mutation contained in the DNA component of the RNA-DNA oligonucleotide or the heterologous region can be transferred to the plant genome, resulting in a “mutant” gene that, for example, is not induced in response to a stress and, therefore, does not confer the maladaptive phenotype. Such a method similarly can be used to knock-out the activity of a stress-regulated gene, for example, in an undesirable plant. Such a method can provide the advantage that a desirable wild-type plant need not compete with the undesirable plant, for example, for light, nutrients, or the like.

A method of modulating the responsiveness of a plant cell to a stress condition also can be performed by introducing a mutation in the chromosomal copy of a plant stress-regulated gene, for example, in the stress-regulated regulatory element, by transforming a cell with a chimeric oligonucleotide composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends. An additional feature of the oligonucleotide is the presence of 2′-O-methylation at the RNA residues. The RNA/DNA sequence is designed to align with the sequence of a chromosomal copy of the target regulatory element and to contain the desired nucleotide change (see U.S. Pat. No. 5,501,967, which is incorporated herein by reference).

A plant stress-regulated regulatory element also can be operatively linked to a heterologous polynucleotide such that, upon expression from the regulatory element in the plant cell, confers a desirable phenotype on the plant cell. For example, the heterologous polynucleotide can encode an aptamer, which can bind to a stress-induced polypeptide. Aptamers are nucleic acid molecules that are selected based on their ability to bind to and inhibit the activity of a protein or metabolite. Aptamers can be obtained by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method (see U.S. Pat. No. 5,270,163), wherein a candidate mixture of single stranded nucleic acids having regions of randomized sequence is contacted with a target, and those nucleic acids having a specific affinity to the target are partitioned from the remainder of the candidate mixture, and amplified to yield a ligand enriched mixture. After several iterations a nucleic acid molecule (aptamer) having optimal affinity for the target is obtained. For example, such a nucleic acid molecule can be operatively linked to a plant stress-regulated regulatory element and introduced into a plant. Where the aptamer is selected for binding to a polypeptide that normally is expressed from the regulatory element and is involved in an adaptive response of the plant to a stress, the recombinant molecule comprising the aptamer can be useful for inhibiting the activity of the stress-regulated polypeptide, thereby decreasing the tolerance of the plant to the stress condition.

The invention provides a genetically modified plant, which can be a transgenic plant, that is tolerant or resistant to a stress condition. As used herein, the term “tolerant” or “resistant,” when used in reference to a stress condition of a plant, means that the particular plant, when exposed to a stress condition, shows less of an effect, or no effect, in response to the condition as compared to a corresponding reference plant (naturally occurring wild-type plant or a plant not containing a construct of the present invention). As a consequence, a plant encompassed within the present invention grows better under more widely varying conditions, has higher yields and/or produces more seeds. Thus, a transgenic plant produced according to a method of the invention can demonstrate protection (as compared to a corresponding reference plant) from a delay to complete inhibition of alteration in cellular metabolism, or reduced cell growth or cell death caused by the stress. Preferably, the transgenic plant is capable of substantially normal growth under environmental conditions where the corresponding reference plant shows reduced growth, metabolism or viability, or increased male or female sterility.

The determination that a plant modified according to a method of the invention has increased resistance to a stress-inducing condition can be made by comparing the treated plant with a control (reference) plant using well known methods. For example, a plant having increased tolerance to saline stress can be identified by growing the plant on a medium such as soil, which contains a higher content of salt in the order of at least about 10% compared to a medium the corresponding reference plant is capable of growing on. Advantageously, a plant treated according to a method of the invention can grow on a medium or soil containing at least about 50%, or more than about 75%, particularly at least about more than 100%, and preferably more than about 200% salt than the medium or soil on which a corresponding reference plant can grow. In particular, such a treated plant can grow on medium or soil containing at least 40 mM, generally at least 100 mM, particularly at least 200 mM, and preferably at least 300 mM salt, including, for example, a water soluble inorganic salt such as sodium sulfate, magnesium sulfate, calcium sulfate, sodium chloride, magnesium chloride, calcium chloride, potassium chloride, or the like; salts of agricultural fertilizers, and salts associated with alkaline or acid soil conditions; particularly NaCl.

In another embodiment, the invention provides a plant that is less tolerant or less resistant to a stress condition as compared to a corresponding reference plant. As used herein, the term “less tolerant” or “less resistant,” when used in reference to a stress condition of a plant, means that the particular plant, when exposed to a stress condition, shows an alteration in response to the condition as compared to a corresponding reference plant. As a consequence, such a plant, which generally is an undesirable plant species, is less likely to grow when exposed to a stress condition than an untreated plant.

The present invention also relates to a method of expressing a heterologous nucleotide sequence in a plant cell. Such a method can be performed, for example, by introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell. The heterologous nucleotide sequence can encode a selectable marker, or preferably, a polypeptide that confers a desirable trait upon the plant cell, for example, a polypeptide that improves the nutritional value, digestibility or ornamental value of the plant cell, or a plant comprising the plant cell. Accordingly, the invention provides a transgenic plant that, in response to a stress condition, can produce a heterologous polypeptide from a plant stress-regulated regulatory element. Such transgenic plants can provide the advantage that, when grown in a cold environment for example, expression of the heterologous polypeptide from a plant cold-regulated regulatory element can result in increased nutritional value of the plant.

The present invention further relates to a method of modulating the activity of a biological pathway in a plant cell, wherein the pathway involves a stress-regulated polypeptide. As used herein, reference to a pathway that “involves” a stress-regulated polypeptide means that the polypeptide is required for normal function of the pathway. For example, plant stress-regulated polypeptides as disclosed herein include those acting as kinases or as transcription factors, which are well known to be involved in signal transduction pathways. As such, a method of the invention provides a means to modulate biological pathways involving plant stress-regulated polypeptides, for example, by altering the expression of the polypeptides in response to a stress condition. Thus, a method of the invention can be performed, for example, by introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, thereby modulating the activity of the biological pathway.

A method of the invention can be performed with respect to a pathway involving any of the stress-regulated polypeptides as encoded by a polynucleotide of SEQ ID NOS:1-2703, including for example, a stress-regulated transcription factor, an enzyme, including a kinase, a channel protein (see, for example, Tables 29-31; see, also, Table 1). Pathways in which the disclosed stress-regulated stress factors are involved can be identified, for example, by searching the Munich Information Center for Protein Sequences (MIPS) Arabidopsis thaliana database (MATDB), which is at http://www.mips.biochem.mpg.de/proj/thal/.

The present invention also relates to a method of identifying a polynucleotide that modulates a stress response in a plant cell. Such a method can be performed, for example, by contacting an array of probes representative of a plant cell genome and nucleic acid molecules expressed in plant cell exposed to the stress; detecting a nucleic acid molecule that is expressed at a level different from a level of expression in the absence of the stress; introducing the nucleic acid molecule that is expressed differently into a plant cell; and detecting a modulated response of the plant cell containing the introduced nucleic acid molecule to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell. The contacting is under conditions that allow for selective hybridization of a nucleic acid molecule with probe having sufficient complementarity, for example, under stringent hybridization conditions.

As used herein, the term “array of probes representative of a plant cell genome” means an organized group of oligonucleotide probes that are linked to a solid support, for example, a microchip or a glass slide, wherein the probes can hybridize specifically and selectively to nucleic acid molecules expressed in a plant cell. Such an array is exemplified herein by a GeneChip® Arabidopsis Genome Array (Affymetrix; see Example 1). In general, an array of probes that is “representative” of a plant genome will identify at least about 30% or the expressed nucleic acid molecules in a plant cell, generally at least about 50% or 70%, particularly at least about 80% or 90%, and preferably will identify all of the expressed nucleic acid molecules. It should be recognized that the greater the representation, the more likely all nucleotide sequences of cluster of stress-regulated genes will be identified.

A method of the invention is exemplified in Example 1, wherein clusters of Arabidopsis genes induced to cold, to increased salinity, to increased osmotic pressure, and to a combination of the above three stress conditions were identified. Based on the present disclosure, the artisan readily can obtain nucleic acid samples for Arabidopsis plants exposed to other stress conditions, or combinations of stress conditions, and identify clusters of genes induced in response to the stress conditions. Similarly, the method is readily adaptable to identifying clusters of stress-regulated genes expressed in other plant species, particularly commercially valuable plant species, where a substantial amount of information is known regarding the genome.

The clusters of genes identified herein include those clusters of genes that are induced or repressed in response to a combination of stress conditions, but not to any of the stress conditions alone; and clusters of genes that are induced or repressed in response to a selected stress condition, but not to other stress conditions tested. Furthermore, clusters of genes that respond to a stress condition in a temporally regulated manner are also included, such as gene clusters that are induced early (for example, within about 3 hours), late (for example, after about 8 to 24 hours), or continuously in a stress response. In addition, the genes within a cluster are represented by a variety of cellular proteins, including transcription factors, enzymes such as kinases, channel proteins, and the like (see Tables 1 and 29-31). Thus, the present invention further characterizes nucleotide sequences that previously were known to encode cellular peptides by classifying them within clusters of stress-regulated genes.

The present invention additionally relates to a method of identifying a stress condition to which a plant cell was exposed. Such a method can be performed, for example, by contacting nucleic acid molecules expressed in the plant cell and an array of probes representative of the plant cell genome; and detecting a profile of expressed nucleic acid molecules characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed. The contacting generally is under conditions that allow for selective hybridization of a nucleic acid molecule with probe having sufficient complementarity, for example, under stringent hybridization conditions. The profile can be characteristic of exposure to a single stress condition, for example, an abnormal level of cold, osmotic pressure, or salinity (Tables 3-14), or can be characteristic of exposure to more than one stress condition (Tables 15-26, for example, cold, increased osmotic pressure and increased salinity (see Tables 24-26).

The method can be practiced using at least one nucleic acid probe and can identify one or combination of stress conditions by detecting altered expression of one or a plurality of polynucleotides representative of plant stress-regulated genes. As used herein, the term “at least one” includes one, two, three or more, for example, five, ten, twenty, fifty or more polynucleotides, nucleic acid probes, and the like. The term “plurality” is used herein to mean two or more, for example, three, four, five or more, including ten, twenty, fifty or more polynucleotides, nucleic acid probes, and the like.

In a method of the invention, nucleic acid samples from the plant cells to be collected can be contacted with an array, then the profile can be compared with known expression profiles prepared from nucleic acid samples of plants exposed to a known stress condition or combination of stress conditions. By creating a panel of such profiles, representative of various stress conditions, an unknown stress condition to which a plant was exposed can be identified simply by comparing the unknown profile with the known profiles and determining which known profile that matches the unknown profile. Preferably, the comparison is automated. Such a method can be useful, for example, to identify a cause of damage to a crop, where the condition causing the stress is not known or gradually increases over time. For example, accumulation in soils over time of salts from irrigation water can result in gradually decreasing crop yields. Because the accumulation is gradual, the cause of the decreased yield may not be readily apparent. Using the present methods, it is possible to evaluate the stress to which the plants are exposed, thus revealing the cause of the decreased yields.

The present invention, therefore includes a computer readable medium containing executable instructions form receiving expression data for sequences substantially similar to any of those disclosed herein and comparing expression data from a test plant to a reference plant that has been exposed to an abiotic stress. Also provided is a computer-readable medium containing sequence data for sequences substantially similar to any of the sequences described herein, or the complements thereof, and a module for comparing such sequences to other nucleic acid sequences.

Also provided are plants and plant cells comprising plant stress-regulatory elements of the present invention operably linked to a nucleotide sequence encoding a detectable signal. Such plants can be used as diagnostic or “sentinel” plants to provide early warning that nearby plants are being stressed so that appropriate actions can be taken. In one embodiment, the signal is one that alters the appearance of the plant. For example, an osmotic stress regulatory element of the present invention can be operably linked to a nucleotide sequence encoding a fluorescent protein such as green fluorescent protein. When subjected to osmotic stress, the expression of the green fluorescent protein in the sentinel plant provides a visible signal so that appropriate actions can be taken to remove or alleviate the stress. The use of fluorescent proteins in plants is well known (see, for example, in Leffel et al., BioTechniques 23:912, 1997).

The invention further relates to a method of identifying an agent that modulates the activity of a stress-regulated regulatory element of a plant. As used herein, the term “modulate the activity,” when used in reference to a plant stress-regulated regulatory element, means that expression of a polynucleotide from the regulatory element is increased or decreased. In particular, expression can be increased or decreased with respect to the basal activity of the promoter, i.e., the level of expression, if any, in the absence of a stress condition that normally induces expression from the regulatory element; or can be increased or decreased with respect to the level of expression in the presence of the inducing stress condition. As such, an agent can act as a mimic of a stress condition, or can act to modulate the response to a stress condition.

Such a method can be performed, for example, by contacting the regulatory element with an agent suspected of having the ability to modulate the activity of the regulatory element, and detecting a change in the activity of the regulatory element. In one embodiment, the regulatory element can be operatively linked to a heterologous polynucleotide encoding a reporter molecule, and an agent that modulates the activity of the stress-regulated regulatory element can be identified by detecting a change in expression of the reporter molecule due to contacting the regulatory element with the agent. Such a method can be performed in vitro in a plant cell-free system, or in a plant cell in culture or in a plant in situ.

A method of the invention also can be performed by contacting the agent is contacted with a genetically modified cell or a transgenic plant containing an introduced plant stress-regulated regulatory element, and an agent that modulates the activity of the regulatory element is identified by detecting a phenotypic change in the modified cell or transgenic plant.

A method of the invention can be performed in the presence or absence of the stress condition to which the particularly regulatory element is responsive. As such, the method can identify an agent that modulates the activity of plant stress-regulated promoter in response to the stress, for example, an agent that can enhance the stress response or can reduce the stress response. In particular, a method of the invention can identify an agent that selectively activates the stress-regulated regulatory elements of a cluster of plant stress-regulated genes, but does not affect the activity of other stress-regulated regulatory genes. As such, the method provides a means to identify an agent that acts as a stress mimic. Such agents can be particularly useful to prepare a plant to an expected stress condition. For example, a agent that acts as a cold mimic can be applied to a field of plants prior to the arrival of an expected cold front. Thus, the cold stress response can be induced prior to the actual cold weather, thereby providing the plants with the protection of the stress response, without the plants suffering from any initial damage due to the cold. Similarly, an osmotic pressure mimic can be applied to a crop of plants prior a field being flooded by a rising river.

In one embodiment, the present invention provides a method for marker-assisted selection. Marker-assisted selection involves the selection of plants having desirable phenotypes based on the presence of particular nucleotide sequences (“markers”). The use of markers allows plants to be selected early in development, often before the phenotype would normally be manifest. Because it allows for early selection, marker-assisted selection decreases the amount of time need for selection and thus allows more rapid genetic progress.

Briefly, marker-assisted selection involves obtaining nucleic acid from a plant to be selected. The nucleic acid obtained is then probed with probes that selectively hybridize under stringent, preferably highly stringent, conditions to a nucleotide sequence or sequences associated with the desired phenotype. In one embodiment, the probes hybridize to any of the stress-responsive genes or regulatory regions disclosed herein, for example, any one of SEQ ID NOS:1-2703. The presence of any hybridization products formed is detected and plants are then selected on the presence or absence of the hybridization products.

The following examples are intended to illustrate but not limit the invention.

Example 1 Profiling of Plant Stress-Regulated Genes

This example demonstrates that clusters of stress-regulated genes can be identified in plant cells exposed to various stress conditions, either alone or in combination.

A GeneChip® Arabidopsis Genome Array (Affymetrix, Santa Clara, Calif.) was used to identify clusters of genes that were coordinately induced in response to various stress conditions. The GeneChip® Arabidopsis Genome Array contains probes synthesized in situ and is designed to measure temporal and spatial gene expression of approximately 8700 genes in greater than 100 EST clusters. The sequences used to develop the array were obtained from GenBank (http://www.ncbi.nlm.nih.gov/) in collaboration with Torrey Mesa Research Institute (San Diego, Calif.), formerly known as Novartis Agriculture Discovery Institute. Eighty percent of the nucleotide sequences represented on the array are predicted coding sequences from genomic BAC entries; twenty percent are high quality cDNA sequences. The array also contains over 100 EST clusters that share homology with the predicted coding sequences from BAC clones (see, for example, world wide web at address (url) “affymetrix.com/products/Arabidopsis_content.html”.

The Affymetrix GeneChip® array was used to define nucleotide sequences/pathways affected by various abiotic stresses and to define which are uniquely regulated by one stress and those that respond to multiple stress, and to identify candidate nucleotide sequences for screening for insertional mutants. Of the approximately 8,700 nucleotide sequences represented on the Affymetrix GeneChip® array, 2862 nucleotide sequences showed at least a 2-fold change in expression in at least one sample, relative to no-treatment controls. Of those 2,862 nucleotide sequences 1,335 were regulated only by cold stress, 166 were regulated only mannitol stress and 209 were regulated only by saline stress. Furthermore, of the 2,862 nucleotide sequences 123 nucleotide sequences were regulated by salt and mannitol stress, 293 were regulated by mannitol and cold stress, 274 were regulated by cold and saline stress and 462 were regulated by cold, mannitol and salt. Of the 2,862 nucleotide sequences, 771 passed the higher stringency of showing at least a 2-fold change in expression in at least 2 samples, relative to control. And, 508 of the 771 nucleotide sequences were found in an in-house collection of insertion mutants.

The following describes in more detail how the experiments were done. Transcriptional profiling was performed by hybridizing fluorescence labeled cRNA with the oligonucleotides probes on the chip, washing, and scanning. Each gene is represented on the chip by about sixteen oligonucleotides (25-mers). Expression level is related to fluorescence intensity. Starting material contained 1 to 101 g total RNA; detection specificity was about 1:10⁶; approximately a 2-fold change was detectable, with less than 2% false positive; the dynamic range was approximately 500×. Nucleotide sequences having up to 70% to 80% identity could be discriminated using this system.

Seven day old axenic Arabidopsis seedlings were transferred to Magenta boxes with rafts floating on MS medium. Three weeks later (28 day old seedlings), stresses were applied as follows: Control—no treatment; Cold—Magenta box placed in ice; Mannitol—medium+200 mM mannitol; Salt—medium+100 mM NaCl. Tissue samples were collected at 3 hours and 27 hours into the stress, roots and aerial portions were harvested, RNA was purified, and the samples were analyzed using the GeneChip® Arabidopsis Genome Array (Affymetrix, Santa Clara, Calif.) following the manufacturer's protocol.

Raw fluorescence values as generated by Affymetrix software were processed as follows: the values were brought into Microsoft Excel and values of 25 or less were set to 25 (an empirically determined baseline, Zhu and Wang, Plant Physiol. 124:1472-1476; 2000). The values from the stressed samples were then converted to fold change relative to control by dividing the values from the stressed samples by the values from the no-treatment control samples. Expression patterns that were altered at least 2-fold with respect to the control were selected. This method gave very robust results and resulted in a larger number of nucleotide sequences called as stress-regulated than previous methods had permitted.

Based on the profiles obtained following hybridization of nucleic acid molecules obtained from plant cells exposed to various stress conditions to the probes in the microarray, clusters of nucleotide sequences that were altered in response to the stress conditions were identified (see Tables 3-6, cold responsive; Tables 7-10, salt (saline) responsive; Tables 11 to 14, mannitol (osmotic) responsive; Tables 15-17, cold and mannitol responsive; Tables 18-20, 6 salt and cold responsive; Tables 21-23, salt and mannitol responsive; Tables 24-26, cold, salt and mannitol responsive. Examples of plant gene sequences that varied in expression at least two-fold in response to a combination of cold, saline and osmotic stress in root cells and leaf cells are shown in Tables 27 and 28, respectively. In addition, examples of plant gene sequences that encode transcription factors (Table 29), phosphatases (Table 30), and kinases (Table 31) and that varied at least two-fold in response to a combination of cold, saline and osmotic stress are provided.

Affymetrix ID numbers and corresponding SEQ ID NOS: for the respective Arabidopsis nucleotide sequences are provided Tables 3-26, and can be used to determine SEQ ID NOS: for the sequences shown by Affymetrix ID number in Tables 27-31. The Affymetrix ID number refers to a particular nucleotide sequence on the GeneChip® Arabidopsis Genome Array. In some cases, a particular plant stress-regulated gene sequence hybridized to more than one nucleotide sequence on the GeneChip® Arabidopsis Genome Array (see, for example, Table 3, where SEQ ID NO:36 is shown to have hybridized to the 12187_AT and 15920_I_AT nucleotide sequences on the GeneChip®). In addition, it should be recognized that the disclosed sequences are not limited to coding sequences but, in some cases, include 5′ untranslated sequences (see Table 2) or a longest coding region. As such, while the sequences set forth as SEQ ID NOS:1-2073 generally start with an ATG codon, in most cases each comprises a longer nucleotide sequence, including a regulatory region (see Table 2).

The results disclosed herein demonstrate that several polynucleotides, some of which were known to function as transcription factors, enzymes, and structural proteins, also are involved in the response of a plant cell to stress. The identification of the clusters of stress-regulated genes as disclosed herein provides a means to identify stress-regulated regulatory elements present in Arabidopsis thaliana nucleotide sequences, including consensus regulatory elements. It should be recognized, however that the regulatory elements of the plant genes comprising a sequence as set forth in SEQ ID NOS:156, 229, 233, 558, 573, 606, 625, 635, 787, and 813, which previously have been described as cold regulated genes, are not encompassed within the stress-regulated gene regulatory element of the invention, and the regulatory elements of the plant genes comprising the nucleotide sequences set forth as SEQ ID NOS:1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918, and 1928, which previously have been identified as genes that are responsive to a single stress condition such as cold or saline stress, are not encompassed within the plant stress-regulated gene regulatory elements of the invention to the extent that they confer stress-regulated expression only with respect to the known single stress. Furthermore, the identification of the Arabidopsis stress-regulated genes provides a means to identify the corresponding homologs and orthologs in other plants, including commercially valuable food crops such as wheat, rice, soy, and barley, and ornamental plants. BLASTN and BLASTP searches to identify such sequences revealed the polynucleotide sequences set forth in Table 32, which is on the CD-R compact disc submitted herewith.

Although the invention has been described with reference to the above example, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the claims, which follow Tables 1 to 31.

TABLE 1 SEQUENCE DESCRIPTIONS Seq ID Description 1 unknown protein 2 unknown protein 3 unknown protein 4 putative auxin-induced protein 5 unknown protein 6 hypothetical protein 7 putative protein 8 unknown protein 9 unknown protein 10 unknown protein 11 putative protein 12 Thioredoxin-like protein 13 putative RNA helicase 14 putative protein 15 putative protein 16 RING zinc finger protein, putative 17 putative cyclin 18 putative protein 19 putative protein 20 unknown protein 21 putative protein 22 putative protein 23 hypothetical protein 24 unknown protein 25 hypothetical protein 26 unknown protein 27 unknown protein 28 unknown protein 29 unknown protein 30 putative protein 31 putative protein 32 putative protein 33 unknown protein 34 putative ribonuclease III 35 unknown protein 36 unknown protein 37 unknown protein 38 unknown protein 39 unknown protein 40 putative histidine kinase 41 scarecrow-like 7 (SCL7) 42 putative protein 43 No function assigned by TIGR 44 unknown protein 45 unknown protein 46 succinyl-CoA-ligase alpha subunit 47 putative protein 48 CLV1 receptor kinase like protein 49 putative receptor-like protein kinase 50 putative squalene synthase 51 putative receptor protein kinase 52 somatic embryogenesis receptor- like kinase, putative 53 putative protein 54 putative beta-glucosidase 55 multi-drug resistance protein 56 receptor protein kinase (TMK1), putative 57 putative receptor-like protein kinase 58 putative pectate lyase 59 putative protein kinase 60 putative peroxidase 61 cytochrome P450-like protein 62 putative beta-amylase 63 monosaccharide transporter STP3 64 Lycopersicon esculentum proteinase TMP, Pir2:T07617 65 putative receptor-like protein kinase 66 G-box-binding factor 1 67 amino acid carrier, putative 68 myb-related protein 69 No function assigned by TIGR 70 SNF1 like protein kinase 71 Cu/Zn superoxide dismutase-like protein 72 putative protein kinase 73 small nuclear ribonucleoprotein U1A 74 ras-like GTP-binding protein 75 oleoyl-[acyl-carrier-protein] hydrolase-like protein 76 putative heat shock transcription factor 77 putative protein 78 membrane-bound small GTP-binding-like protein 79 putative protein (fragment) 80 indole-3-acetate beta- glucosyltransferase like protein 81 HD-zip transcription factor (athb-8) 82 putative cAMP-dependent protein kinase 83 glucuronosyl transferase- like protein 84 putative leucine-rich repeat disease resistance protein 85 98b like protein 86 putative receptor-like protein kinase 87 IAA-Ala hydrolase (IAR3) 88 putative AP2 domain transcription factor 89 putative expansin 90 putative Ap2 domain protein 91 expansin (At-EXP1) 92 cytochrome P450-like protein 93 putative ATP-dependent RNA helicase A 94 unknown protein 95 predicted protein 96 putative glucosyltransferase 97 unknown protein 98 putative xyloglucan- specific glucanase 99 cysteine synthase 100 clathrin assembly protein AP19 homolog 101 dynein light chain like protein 102 chaperonin CPN10 103 putative bHLH transcription factor 104 putative glyoxysomal malate dehydrogenase precursor 105 ATP-dependent RNA helicase, putative 106 chlorophyll synthetase 107 similar to epoxide hydrolases 108 putative protein 109 unknown protein 110 hypothetical protein 111 putative membrane transporter 112 putative tyrosyl-tRNA synthetase 113 ARGININE/SERINE-RICH SPLICING FACTOR RSP31 114 putative oxidoreductase 115 unknown protein 116 linker histone protein, putative 117 hypothetical protein 118 putative protein 119 putative mitochondrial carrier protein 120 putative transcription factor 121 MYB-related protein 122 myb-related transcription factor, putative 123 unknown protein 124 unknown protein 125 putative glycine-rich protein 126 No function assigned by TIGR 127 unknown protein 128 unknown protein 129 unknown protein 130 unknown protein 131 putative membrane channel protein 132 putative protein 133 unknown protein 134 gamma glutamyl hydrolase, putative 135 40S ribosomal protein S5 136 DnaJ-like protein 137 40S ribosomal protein S26 138 putative WRKY-type DNA binding protein 139 putative protein 140 hypothetical protein 141 putative ubiquitin- conjugating enzyme 142 peptidylprolyl isomerase ROC1 143 glyceraldehyde-3- phosphate dehydrogenase C subunit (GapC) 144 No function assigned by TIGR 145 putative protein 146 putative thioredoxin 147 thioredoxin h, putative 148 thioredoxin-like 149 allene oxide synthase (emb|CAA73184.1) 150 anthranilate synthase component I-1 precursor (sp|P32068) 151 CELL DIVISION CONTROL PROTEIN 2 HOMOLOG A 152 protein kinase cdc2 homolog B 153 ethylene responsive element binding factor 1 (frameshift !) 154 ethylene responsive element binding factor 2 (ATERF2) (sp|O80338) 155 ethylene responsive element binding factor 5 (ATERF5) (sp|O80341) 156 glucose-6-phosphate dehydrogenase 157 photomorphogenesis repressor (COP1) 158 unknown protein 159 DNA (cytosine-5)- methyltransferase (DNA methyltransferase) (DNA metase) (sp|P34881) 160 PROLIFERA 161 putative photomorphogenesis repressor protein 162 SNF1-like protein kinase(Akin11) 163 thioredoxin h 164 thioredoxin 165 Ca2+-dependent lipid-binding protein, putative 166 putative auxin-induced protein 167 putative bZIP transcription factor 168 hypothetical protein 169 putative AVR9 elicitor response protein 170 putative serine/threonine protein kinase 171 bZIP transcription factor ATB2 172 putative spliceosome associated protein 173 3-hydroxyisobutyryl-coenzyme A hydrolase-like protein 174 putative protein 175 putative Mutator-like transposase 176 putative protein 177 unknown protein 178 putative protein 179 putative protein 180 putative galactinol synthase 181 putative transcriptional regulator 182 nuclear matrix constituent protein 1 (NMCP1)-like 183 putative DNA-binding protein RAV2 184 No function assigned by TIGR 185 basic blue protein, 5′ partial 186 unknown protein 187 putative calcium-binding protein, calreticulin 188 putative pyrophosphate-fructose-6- phosphate 1-phosphotransferase 189 ribosomal protein L11, cytosolic 190 putative dTDP-glucose 4-6- dehydratase 191 40S ribosomal protein S20-like protein 192 60S ribosomal protein L24 193 coatomer-like protein, epsilon subunit 194 glycoprotein(EP1), putative 195 putative SPLI-related protein 196 unknown protein 197 putative transport protein SEC61 beta-subunit 198 unknown protein 199 putative cytochrome P450 200 UTP-glucose glucosyltransferase-like protein 201 60S ribosomal protein L23 202 40S ribosomal protein S17 203 40S ribosomal protein S26 204 protein translation factor Suil homolog, putative 205 unknown protein 206 gamma glutamyl hydrolase, putative 207 dTDP-glucose 4,6- dehydratase, putative 208 extensin-like protein 209 unknown protein 210 protein phosphatase 2C- like protein 211 ubiquitin-like protein 212 protein phosphatase 2C-like protein 213 unknown protein 214 putative RING zinc finger ankyrin protein 215 unknown protein 216 putative rubisco subunit binding-protein alpha subunit 217 putative acetone- cyanohydrin lyase 218 putative isoamylase 219 putative protein 220 HSP associated protein like 221 60S ribosomal protein L39 222 unknown protein 223 putative SF16 protein {Helianthus annuus} 224 unknown protein 225 thioredoxin 226 trehalose-6-phosphate phosphatase (AtTPPB) 227 chlorophyll a/b-binding protein 228 class IV chitinase (CHIV) 229 chalcone synthase (naringenin- chalcone synthase) (testa 4 protein) (sp|P13114) 230 unknown protein 231 cinnamyl-alcohol dehydrogenase ELI3-2 232 farnesyl-pyrophosphate synthetase FPS2 233 phospholipid hydroperoxide glutathione peroxidase 234 heat shock transcription factor HSF4 235 heat shock protein 101 236 17.6 kDa heat shock protein (AA 1-156) 237 heat shock protein 17.6A 238 heat-shock protein 239 HY5 240 putative auxin-induced protein, IAA12 241 early auxin-induced protein, IAA19 242 auxin-inducible gene (IAA2) 243 putative protein 244 putative choline kinase 245 thymidylate kinase-like protein 246 CTP synthase like protein 247 putative protein 248 putative amidase 249 4-alpha-glucanotransferase 250 hypothetical protein 251 similar to auxin-induced protein 252 putative protein 253 putative protein 254 putative protein 255 hyuC-like protein 256 putative tetracycline transporter protein 257 similar to early nodulins 258 putative protein 259 putative peptidyl-prolyl cis- trans isomerase 260 unknown protein 261 unknown protein 262 putative endochitinase 263 putative ABC transporter 264 No function assigned by TIGR 265 CONSTANS-like B-box zinc finger protein 266 unknown protein 267 unknown protein 268 putative mitochondrial processing peptidase alpha subunit 269 putative pre-mRNA splicing factor 270 putative phosphatidylserine decarboxylase 271 unknown protein 272 unknown protein 273 unknown protein 274 putative casein kinase I 275 unknown protein 276 60S ribosomal protein L23A 277 putative mitochondrial dicarboxylate carrier protein 278 enoyl-ACP reductase (enr- A) 279 putative isoamylase 280 formamidase-like protein 281 reticuline oxidase-like protein 282 unknown protein 283 putative transketolase precursor 284 putative protein 285 unknown protein 286 unknown protein 287 unknown protein 288 putative esterase D 289 predicted protein of unknown function 290 unknown protein 291 putative indole-3-glycerol phosphate synthase 292 isopentenyl pyrophosphate:dimethyllallyl pyrophosphate isomerase 293 kinase associated protein phosphatase 294 putative K+ channel, beta subunit 295 KNAT1 homeobox-like protein 296 PSI type II chlorophyll a/b-binding protein, putative 297 transcription factor 298 putative WD-40 repeat protein, MSI2 299 WD-40 repeat protein (MSI3) 300 putative WD-40 repeat protein, MSI4 301 unknown protein 302 hypothetical protein 303 putative protein 304 No function assigned by TIGR 305 polyphosphoinositide binding protein, putative 306 hypothetical protein 307 unknown protein 308 chloroplast ribosomal L1-like protein 309 cold-regulated protein cor15b precursor 310 cyanohydrin lyase like protein 311 putative replication protein Al 312 putative protein 313 possible apospory-associated like protein 314 DNA binding protein GT-1, putative 315 AT-hook DNA-binding protein (AHP1) 316 putative phospholipase 317 chloroplast FtsH protease, putative 318 enoyl-CoA hydratase like protein 319 berberine bridge enzyme- like protein 320 putative sugar transporter 321 unknown protein 322 No function assigned by TIGR 323 hypothetical protein 324 putative acidic ribosomal protein 325 putative protein 326 unknown protein 327 hypothetical protein 328 putative protein 329 dihydroxypolyprenyl benzoate methyltransferase 330 unknown protein 331 myb-related protein 332 No function assigned by TIGR 333 putative protein 334 putative disease resistance response protein 335 hypothetical protein 336 No function assigned by TIGR 337 starch branching enzyme II 338 No function assigned by TIGR 339 putative enolase (2- phospho-D-glycerate hydroylase) 340 putative protein kinase 341 HD-Zip protein, putative 342 putative protein kinase 343 phenylalanyl-trna synthetase-like protein 344 putative aconitase 345 NAM(no apical meristem) protein, putative 346 unknown protein 347 putative phosphomannomutase 348 putative farnesylated protein 349 unknown protein 350 water stress-induced protein, putative 351 unknown protein 352 unknown protein 353 PEROXISOMAL MEMBRANE PROTEIN PMP22 354 putative peroxisomal membrane carrier protein 355 putative protein 356 unknown protein 357 putative protein 358 putative protein 359 argininosuccinate synthase-like protein 360 1-phosphatidylinositol-4,5- bisphosphate phosphodiesterase 361 putative JUN kinase activator protein 362 putative 60S ribosomal protein L35 363 nucleoid DNA-binding protein cnd41-like protein 364 SigA binding protein 365 hypothetical protein 366 putative protein kinase 367 unknown protein 368 regulatory protein NPR1-like; transcription factor inhibitor I kappa B-like 369 putative protein 370 hypothetical protein 371 phosphoribosylanthranilate isomerase 372 phosphoribosylanthranilate isomerase 373 sterol glucosyltransferase, putative 374 putative gigantea protein 375 putative MYB family transcription factor 376 hypothetical protein 377 hypothetical protein 378 predicted protein 379 cytochrome P450, putative 380 putative Na+ dependent ileal bile acid transporter 381 unknown protein 382 RING-H2 finger protein RHF1a 383 putative protein 384 unknown protein 385 putative protein 386 putative auxin-regulated protein 387 hypothetical protein 388 unknown protein 389 unknown protein 390 putative protein 391 putative protein 392 unknown protein 393 histone H1 394 Argonaute (AGO 1)-like protein 395 unknown protein 396 putative protein with C- terminal RING finger 397 unknown protein 398 unknown protein 399 unknown protein 400 unknown protein 401 unknown protein 402 putative copper amine oxidase 403 unknown protein 404 unknown protein 405 unknown protein 406 putative protein 407 putative protein 408 unknown protein 409 unknown protein 410 putative protein 411 putative protein 412 unknown protein 413 serine/threonine kinase- like protein 414 alcohol dehydrogenase, putative 415 anthranilate phosphoribosyltransferase, chloroplast precursor (sp|Q02166) 416 phytochrome C (sp|P14714) 417 putative phytochrome-associated protein 3 418 receptor serine/threonine kinase PR5K 419 Ran-binding protein (atranbp1a) 420 small Ras-like GTP-binding protein (gb|AAB58478.1) 421 sterol-C5-desaturase 422 tryptophan synthase beta chain 1 precursor (sp|P14671) 423 thioredoxin f2 (gb|AAD35004.1) 424 No function assigned by TIGR 425 putative WRKY DNA-binding protein 426 putative protein 427 unknown protein 428 unknown protein 429 14-3-3 protein homolog RCI1 (pir||S47969) 430 unknown protein 431 putative CCCH-type zinc finger protein 432 PINHEAD (gb|AAD40098.1); translation initiation factor 433 plasma membrane proton ATPase (PMA) 434 CHLOROPHYLL A-B BINDING PROTEIN 4 PRECURSOR homolog 435 membrane related protein CP5, putative 436 ABC transporter (AtMRP2) 437 putative embryo-abundant protein 438 putative anthocyanidin-3-glucoside rhamnosyltransferase 439 putative lipid transfer protein 440 unknown protein 441 unknown protein 442 galactinol synthase, putative 443 putative protein 444 putative protein 445 SCARECROW-like protein 446 unknown protein 447 unknown protein 448 unknown protein 449 unknown protein 450 asparagine-tRNA ligase 451 putative protein 452 glutamate-1-semialdehyde 2,1-aminomutase 1 precursor (GSA 1) (glutamate-1-semialdehyde aminotransferase 1) (GSA- AT 1) (sp|P42799) 453 hypothetical protein 454 putative serine protease-like protein 455 No function assigned by TIGR 456 unknown protein 457 unknown protein 458 gamma-adaptin, putative 459 UDP rhamnose- anthocyanidin-3-glucoside rhamnosyltransferase-like protein 460 carbonate dehydratase-like protein 461 putative microtubule- associated protein 462 putative ribophorin I 463 putative zinc finger protein 464 chloroplast FtsH protease, putative 465 putative protein 466 unknown protein 467 putative LEA protein 468 putative protein 469 putative protein 470 unknown protein 471 putative purple acid phosphatase 472 unknown protein 473 putative protein 474 unknown protein 475 chlorophyll binding protein, putative 476 phosphoenolpyruvate carboxylase (PPC) 477 chlorophyll a/b-binding protein- like 478 AtAGP4 479 putative cryptochrome 2 apoprotein 480 type 2 peroxiredoxin, putative 481 Atpm24.1 glutathione S transferase 482 delta tonoplast integral protein (delta-TIP) 483 20S proteasome subunit (PAA2) 484 dormancy-associated protein, putative 485 putative cytidine deaminase 486 No function assigned by TIGR 487 putative phospholipase D-gamma 488 cell elongation protein, Dwarf1 489 germin-like protein 490 hevein-like protein precursor (PR- 4) 491 rac-like GTP binding protein (ARAC5) 492 phosphoprotein phosphatase, type 1 catalytic subunit 493 ubiquitin-protein ligase UBC9 494 xyloglucan endotransglycosylase- related protein XTR-7 495 cysteine synthase 496 putative villin 2 497 glutathione S-transferase 498 5-adenylylsulfate reductase 499 arginine decarboxylase 500 ATHP2, putative 501 ornithine carbamoyltransferase precursor 502 puative protein 503 putative protein 504 unknown protein 505 putative protein 506 putative protein 507 unknown protein 508 unknown protein 509 unknown protein 510 unknown protein 511 hypothetical protein 512 putative protein 513 putative DnaJ protein 514 plastocyanin 515 unknown protein 516 unknown protein 517 unknown protein 518 unknown protein 519 unknown protein 520 unknown protein 521 putative ATP-dependent RNA helicase 522 non-race specific disease resistance protein (NDR1) 523 hypothetical protein 524 putative protein 525 putative protein 526 putative protein 527 copper transport protein 528 putative protein 529 unknown protein 530 unknown protein 531 unknown protein 532 putative protein kinase 533 unknown protein 534 putative protein 535 putative protein 536 hypothetical protein 537 putative protein 538 putative AP2 domain transcription factor 539 putative nitrilase 540 putative protein 541 putative tetrahydrofolate synthase 542 heat-shock protein 543 unkown protein 544 unknown protein 545 histone H4 546 hypothetical protein 547 unknown protein 548 putative protein 549 predicted protein 550 putative dihydrolipoamide succinyltransferase 551 actin3 552 putative CCCH-type zinc finger protein 553 MAP kinase kinase 2 554 ethylene-insensitive3-like 1 (EIL1) 555 histidine transport protein (PTR2- B) 556 putative auxin-induced protein AUX2-11 557 hydroxyacylglutathione hydrolase cytoplasmic (glyoxalase II) (GLX II) 558 delta-8 sphingolipid desaturase 559 cellulose synthase catalytic subunit (Ath-A) 560 nitrate transporter (NTL1) 561 DNA-binding homeotic protein Athb-2 562 hypothetical protein 563 aspartate aminotransferase 564 4-coumarate:CoA ligase 1 565 pyruvate dehydrogenase E1 beta subunit, putative 566 nucleotide diphosphate kinase Ia (emb|CAB58230.1) 567 chloroplast Cpn21 protein 568 ATP dependent copper transporter 569 very-long-chain fatty acid condensing enzyme (CUT1) 570 putative purine-rich single-stranded DNA-binding protein 571 serine/threonine protein phosphatase (type 2A) 572 isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP2) 573 putative c2h2 zinc finger transcription factor 574 putative 20S proteasome beta subunit PBC2 575 nucleoside diphosphate kinase 3 (ndpk3) 576 ras-related small GTP-binding protein 577 putative 4-coumarate:CoA ligase 2 578 transcription factor HBP-1b homolog (sp|P43273) 579 biotin synthase (Bio B) 580 homeobox protein HAT22 581 putative preprotein translocase SECY protein 582 carbamoylphosphate synthetase, putative 583 putative protein kinase, ADK 1 584 putative nuclear DNA-binding protein G2p 585 hypothetical protein 586 hypothetical protein 587 unknown protein 588 unknown protein 589 molybdopterin synthase (CNX2) 590 putative ribosomal protein L6 591 unknown protein 592 En/Spm-like transposon protein 593 putative protein 594 putative protein 595 unknown protein 596 hypothetical protein 597 unknown protein 598 unknown protein 599 putative lysosomal acid lipase 600 unknown protein 601 unknown protein 602 NifS-like aminotranfserase 603 actin 8 604 hypothetical protein 605 putative protein 606 heat-shock protein (At- hsc70-3) 607 putative protein disulfide isomerase precursor 608 adenosine nucleotide translocator 609 photosystem II oxygen-evolving complex protein 3-like 610 sedoheptulose-bisphosphatase precursor 611 glutathione S-transferase (GST6) 612 geranylgeranyl reductase 613 hypothetical protein 614 hypothetical protein 615 phosphoribulokinase precursor 616 high mobility group protein (HMG1), putative 617 protease inhibitor II 618 protease inhibitor II 619 cytochrome P450 90A1 (sp|Q42569) 620 unknown protein 621 heat shock protein 90 622 tubulin beta-9 chain 623 putative ubiquitin carboxyl terminal hydrolase 624 protein kinase 625 DRE/CRT-binding protein DREB1C 626 histidyl-tRNA synthetase 627 splicing factor, putative 628 glutamyl-tRNA synthetase 629 putative RING zinc finger protein 630 phytochelatin synthase (gb|AAD41794.1) 631 putative C2H2-type zinc finger protein 632 putative ligand-gated ion channel protein 633 putative ribosomal-protein S6 kinase (ATPK6) 634 MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN 635 temperature-sensitive omega-3 fatty acid desaturase, chloroplast precursor (sp|P48622) 636 adenylosuccinate synthetase 637 putative 14-3-3 protein 638 putative cytochrome P450 639 putative two-component response regulator 3 protein 640 putative RING-H2 zinc finger protein ATL6 641 No function assigned by TIGR 642 small zinc finger-like protein 643 hypothetical protein 644 MAP kinase (ATMPK6) 645 vacuolar ATP synthase, putative 646 kinesin-like protein 647 serine/threonine-specific protein kinase NAK 648 No function assigned by TIGR 649 ACTIN 2/7 (sp|P53492) 650 phosphoglycerate kinase, putative 651 homeotic protein BEL1 homolog 652 proline iminopeptidase 653 pasticcino 1 654 serine/threonine protein kinase 655 cytochrome P450 monooxygenase (CYP71B4) 656 No function assigned by TIGR 657 putative GDSL-motif lipase/hydrolase 658 putative protein 659 unknown protein 660 hypothetical protein 661 putative glycosylation enzyme 662 No function assigned by TIGR 663 No function assigned by TIGR 664 unknown protein 665 putative ABC transporter 666 nifU-like protein 667 putative receptor-like protein kinase 668 putative disease resistance protein 669 receptor-like protein kinase-like 670 ubiquitin activating enzyme 2 (gb|AAB37569.1) 671 No function assigned by TIGR 672 putative receptor-like protein kinase 673 K+ transporter, AKT1 674 shaggy-like kinase beta 675 heat shock protein 70 676 plasma membrane intrinsic protein 1a 677 HSP90-like protein 678 histone H1, putative 679 unknown protein 680 dnaK-type molecular chaperone hsc70.1-like 681 gamma-glutamylcysteine synthetase 682 peroxidase (ATP22a) 683 putative serine carboxypeptidase precursor 684 putative dioxygenase 685 glucose transporter 686 NOI protein, nitrate-induced 687 putative protein 688 putative protein 689 unknown protein 690 putative photosystem I reaction center subunit II precursor 691 putative protein 692 unknown protein 693 cobalamin biosynthesis protein 694 adenine nucleotide translocase 695 glutathione transferase, putative 696 putative 60S ribosomal protein L21 697 cytochrome P450 like protein 698 cytochrome b245 beta chain homlog RbohApl08, putative 699 RNA helicase, DRH1 700 putative aldolase 701 farnesyltransferase subunit A (FTA) 702 No function assigned by TIGR 703 putative putative sister- chromatide cohesion protein 704 calcium-dependent protein kinase 705 serine/threonine protein phosphatase type 2A, putative 706 40S ribosomal protein S28 (sp|P34789) 707 RNA polymerase subunit 708 DNA-damage- repair/toleration protein DRT102 709 putative C2H2-type zinc finger protein 710 putative adenosine phosphosulfate kinase 711 lipase 712 putative violaxanthin de- epoxidase precursor (U44133) 713 aromatic rich glycoprotein, putative 714 putative fumarase 715 flavonol synthase (FLS) (sp|Q96330) 716 response regulator 5, putative 717 sulfate transporter 718 putative floral homeotic protein, AGL9 719 putative ethylene-inducible protein 720 C-8,7 sterol isomerase 721 TCH4 protein (gb|AAA92363.1) 722 hypothetical protein 723 putative urease accessory protein 724 molybdopterin synthase sulphurylase (gb|AAD18050.1) 725 putative protein 726 NBD-like protein (gb|AAD20643.1) 727 AtHVA22c 728 unknown protein 729 phytoene synthase (gb|AAB65697.1) 730 protein kinase (AME2/AFC1) 731 hypothetical protein 732 cyclin-dependent protein kinase- like protein 733 photosystem II stability/assembly factor HCF136 (sp|O82660) 734 hypothetical protein 735 DNA binding-like protein 736 putative protein 737 chorismate mutase 738 putative LRR receptor protein kinase 739 putative chalcone synthase 740 putative protein kinase 741 replicase, putative 742 putative cysteine proteinase 743 60S ribosomal protein L36 744 unknown protein 745 CLC-b chloride channel protein 746 putative ribosomal protein S14 747 histone H2B like protein (emb|CAA69025.1) 748 60S ribosomal protein L2 749 60S ribosomal protein L15 homolog 750 ribosomal protein S27 751 ribosomal protein 752 60S ribosomal protein L12 753 60s ribosomal protein L34 754 putative ribosomal protein S10 755 drought-induced protein like 756 blue copper-binding protein, 15K (lamin) 757 calmodulin-like protein 758 putative protein 759 No function assigned by TIGR 760 alpha-mannosidase, putative 761 uncoupling protein (ucp/PUMP) 762 homeodomain-like protein 763 ribosomal protein S18, putative 764 similar to SOR1 from the fungus Cercospora nicotianae 765 60S ribosomal protein L13, BBC1 protein 766 50S ribosomal protein L24, chloroplast precursor 767 putative ribosomal protein 768 unknown protein 769 aspartate aminotransferase (AAT1) 770 potassium channel protein AtKC 771 unknown protein 772 peroxisomal targeting signal type 2 receptor 773 putative protein 774 Ras-related GTP-binding protein (ARA-4) 775 S-receptor kinase homolog 2 precursor 776 pathogenesis-related group 5 protein, putative 777 Nitrilase 4 (sp|P46011) 778 biotin carboxyl carrier protein of acetyl-CoA carboxylase precursor (BCCP) (sp|Q42533) 779 photosystem I reaction centre subunit psaN precursor (PSI-N) (sp|P49107) 780 3(2),5-bisphosphate nucleotidase 781 high affinity Ca2+ antiporter 782 putative cytoskeletal protein 783 putative peroxidase 784 respiratory burst oxidase protein 785 beta-glucosidase 786 calcium-dependent protein kinase (pir||S71196) 787 phosphoinositide specific phospholipase C 788 similarity to S-domain receptor- like protein kinase, Zea mays 789 mitosis-specific cyclin 1b 790 4-coumarate: CoA ligase 3 791 transcription factor IIB (TFIIB) 792 unknown protein 793 hypothetical protein 794 hypothetical protein 795 sugar transporter like protein 796 putative trypsin inhibitor 797 unknown protein 798 putative multispanning membrane protein 799 receptor-like kinase, putative 800 putative inosine-5-monophosphate dehydrogenase 801 inosine-5′-monophosphate dehydrogenase, putative 802 amino acid permease 6 (emb|CAA65051.1) 803 NADPH-ferrihemoprotein reductase (ATR2) 804 putative WRKY-type DNA binding protein 805 putative ankyrin 806 putative hexose transporter 807 aquaporin/MIP-like protein 808 Ser/Thr protein kinase isolog 809 pectate lyase like protein 810 putative 60S ribosomal protein L17 811 putative protein 812 unknown protein 813 phenylalanine ammonia-lyase 814 putative cytochrome P450 monooxygenase 815 ARR1 protein; putative 816 putative bHLH transcription factor 817 aminomethyltransferase-like precursor protein 818 purple acid phosphatase precursor 819 AP2 domain containing protein, putative 820 ubiquitin-conjugating enzyme E2-21 kD 1 (ubiquitin-protein ligase 4) (ubiquitin carrier protein 4) (sp|P42748) 821 translation initiation factor 822 putative VAMP-associated protein 823 spermidine synthase, putative 824 putative protein 825 unknown protein 826 AtKAP alpha 827 glyceraldehyde-3- phosphate dehydrogenase, putative 828 putative poly(A) binding protein 829 alpha-tubulin, putative 830 serine/threonine-specific protein kinase ATPK64 (pir||S20918) 831 putative aspartate-tRNA ligase 832 ras-related small GTP- binding protein RAB1c 833 cycloartenol synthase 834 No function assigned by TIGR 835 cytochrome P450 836 GTPase AtRAB8 837 3-phosphoserine phosphatase 838 transcription factor CRC 839 nuclear cap-binding protein; CBP20 (gb|AAD29697.1) 840 chloroplast membrane protein (ALBINO3) 841 biotin holocarboxylase synthetase 842 expansin AtEx6 843 unknown protein 844 mercaptopyruvate sulfurtransferase, putative 845 putative thiosulfate sulfurtransferase 846 dihydrolipoamide S- acetyltransferase 847 auxin transport protein REH1, putative 848 putative auxin transport protein 849 apyrase (Atapy1) 850 root cap 1 (RCP1) 851 hypothetical protein 852 putative protein 853 predicted protein of unknown function 854 hypothetical protein 855 hypothetical protein 856 hypothetical protein 857 putative aldehyde dehydrogenase 858 putative peroxidase 859 UDP-glucose 4-epimerase-like protein 860 indole-3-acetate beta glucosyltransferase like protein 861 putative beta-1,3-glucanase 862 disease resistance protein-like 863 putative respiratory burst oxidase protein B 864 ubiquitin-conjugating enzyme UBC3 865 cytoplasmic aconitate hydratase 866 NADPH oxidoreductase, putative 867 PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT-like 868 putative protein 869 unknown protein 870 60S acidic ribosomal protein P2 871 No function assigned by TIGR 872 1,4-alpha-glucan branching enzyme protein soform SBE2.2 precursor 873 calcium binding protein (CaBP-22) 874 putative phosphoglucomutase 875 shaggy-like protein kinase etha (EC 2.7.1.—) 876 pyruvate decarboxylase (gb|AAB16855.1) 877 hypothetical protein 878 putative protein kinase 879 putative protein kinase 880 putative leucine aminopeptidase 881 probable cytochrome P450 882 protein kinase 6-like protein 883 arginine methyltransferase (pam1) 884 MYB96 transcription factor-like protein 885 putative protein 886 metal ion transporter 887 No function assigned by TIGR 888 flax rust resistance protein, putative 889 fructose-2,6 bisphosphatase, putative 890 exonuclease RRP41 891 squamosa promoter binding protein-like 2 (emb|CAB56576.1) 892 putative squamosa promoter binding protein 893 O-acetylserine(thiol) lyase, putative 894 snoRNA 895 snoRNA 896 ferredoxin-NADP+ reductase 897 H+-transporting ATP synthase chain 9-like protein 898 photosystem I subunit III precursor, putative 899 photosystem I subunit VI precursor 900 auxin-binding protein 1 precursor 901 putative RAS superfamily GTP- binding protein 902 disease resistance protein-like 903 protein kinase like protein 904 glucuronosyl transferase-like protein 905 putative homeodomain transcription factor 906 putative flavonol reductase 907 putative protein 908 salt-tolerance protein 909 40S ribosomal protein S30 910 putative bZIP transcription factor 911 putative protein 912 putative cinnamoyl CoA reductase 913 unknown protein 914 putative RNA-binding protein 915 phosphatidylinositol synthase (PIS1) 916 unknown protein 917 hydroxyproline-rich glycoprotein homolog 918 50S ribosomal protein L15, chloroplast precursor 919 unknown protein 920 putative YME1 ATP-dependant protease 921 unknown protein 922 putative ribosomal protein L28 923 unknown protein 924 putative protein 925 protein ch-42 precursor, chloroplast 926 protein serine/threonine kinase, putative 927 beta-VPE 928 putative vacuolar sorting receptor 929 putative translation initiation factor IF-2 930 predicted protein of unknown function 931 putative protein 932 hypothetical protein 933 hypothetical protein 934 phosphate transporter, putative 935 No function assigned by TIGR 936 beta subunit of protein farnesyl transferase ERA1 937 putative glutamate decarboxylase 938 putative indole-3-acetate beta-glucosyltransferase 939 putative receptor-like protein kinase 940 UDP-galactose 4- epimerase-like protein 941 putative proliferating cell nuclear antigen, PCNA 942 ubiquitin conjugating enzyme E2 (UBC13) 943 cyclophilin (CYP2) 944 cystatin (emb|CAA03929.1) 945 putative alcohol dehydrogenase 946 acidic ribosomal protein p1 947 glutathione transferase AtGST 10 (emb|CAA10457.1) 948 putative tropinone reductase 949 ZIP4, a putative zinc transporter 950 unknown protein 951 putative protein 952 putative protein 953 putative C2H2-type zinc finger protein 954 putative RING zinc finger protein 955 putative microtubule- associated protein 956 unknown protein 957 putative protein 958 putative protein phosphatase-2c 959 V-ATPase subunit G (vag2 gene) 960 hypothetical protein 961 unknown protein 962 unknown protein 963 unknown protein 964 myrosinase-associated protein, putative 965 hypothetical protein 966 hypothetical protein 967 No function assigned by TIGR 968 unknown protein 969 hypothetical protein 970 LAX1/AUX1-like permease 971 putative UDP-N- acetylglucosamine-dolichyl- phosphate N- acetylglucosaminephosphotransferase 972 chorismate mutase CM2 973 inner mitochondrial membrane protein 974 DEF (CLA1) protein 975 decoy 976 citrate synthase 977 myosin 978 40S ribosomal protein S19 979 ripening-related protein-like 980 putative signal peptidase I 981 methionyl-tRNA synthetase (AtcpMetRS) 982 ribosomal protein precursor-like 983 50S ribosomal protein L21 chloroplast precursor (CL21) 984 putative MYB family transcription factor 985 cyclophilin-like protein 986 hypothetical protein 987 naringenin 3-dioxygenase like protein 988 WD-repeat protein-like protein 989 putative serine carboxypeptidase II 990 prenyltransferase, putative 991 putative ligand-gated ion channel protein 992 clathrin adaptor medium chain protein MU1B, putative 993 No function assigned by TIGR 994 putative Tall-like non- LTR retroelement protein 995 putative 3-isopropylmalate dehydrogenase 996 3-isopropylmalate dehydratase, small subunit 997 unknown protein 998 unknown protein 999 unknown protein 1000 hypothetical protein 1001 putative protein 1002 No function assigned by TIGR 1003 putative beta-glucosidase 1004 putative pectate lyase A11 1005 putative beta-glucosidase 1006 HD-Zip protein 1007 putative ubiquitin conjugating enzyme 1008 homeobox-leucine zipper protein-like 1009 cytochrome P450 like protein 1010 putative cysteine proteinase inhibitor B (cystatin B) 1011 ethylene response sensor (ERS) 1012 putative SWH1 protein 1013 putative glutathione S- transferase 1014 putative protein 1015 unknown protein 1016 putative protein phosphatase 2C 1017 dnaJ protein homolog atj3 1018 ferredoxin 1019 hypothetical protein 1020 putative sugar transport protein, ERD6 1021 putative DnaJ protein 1022 putative AP2 domain transcription factor 1023 putative protein 1024 putative cyclin-dependent kinase regulatory subunit 1025 putative tropinone reductase 1026 signal response protein (GAI) 1027 putative steroid sulfotransferase 1028 hypothetical protein 1029 nucleic acid binding protein-like 1030 putative protein 1031 blue copper binding protein 1032 farnesylated protein (ATFP6) 1033 unknown protein 1034 putative PCF2-like DNA binding protein 1035 teosinte branched1-like protein 1036 putative protein 1037 unknown protein 1038 unknown protein 1039 2-oxoglutarate dehydrogenase, E1 component 1040 unknown protein 1041 unknown protein 1042 CCAAT-binding transcription factor subunit A(CBF-A) 1043 hypothetical protein 1044 putative growth regulator protein 1045 putative presenilin 1046 putative expansin 1047 ribosomal-like protein 1048 unknown protein 1049 unknown protein 1050 putative protein 1051 putative protein 1052 unknown protein 1053 unknown protein 1054 unknown protein 1055 unknown protein 1056 unknown protein 1057 putative protein 1058 putative protein 1059 argininosuccinate lyase (AtArgH) 1060 disease resistance protein homolog 1061 aldehyde dehydrogenase like protein 1062 GBF2, G-box binding factor 1063 CDPK-related kinase 1064 endo-1,4-beta-glucanase 1065 putative serine protease 1066 serine/threonine-specific kinase lecRK1 precursor, lectin receptor-like 1067 putative MAP kinase 1068 RNase L inhibitor-like protein 1069 No function assigned by TIGR 1070 AP2 domain transcription factor 1071 polygalacturonase isoenzyme 1 beta subunit, putative 1072 putative lipid transfer protein 1073 putative protein kinase 1074 putative protein 1075 ATP-dependent RNA helicase like protein 1076 putative cyclic nucleotide- regulated ion channel protein 1077 COP1 like protein 1078 putative peroxidase 1079 putative NAK-like ser/thr protein kinase 1080 putative cytochrome C 1081 cytochrome c 1082 putative serine carboxypeptidase II 1083 acyl-(acyl carrier protein) thioesterase 1084 DNA-binding factor, putative 1085 MAP3K delta-1 protein kinase 1086 AtMlo-hl-like protein 1087 No function assigned by TIGR 1088 putative expansin 1089 defender against cell death protein, putative 1090 glycolate oxidase-like protein 1091 putative ATP-dependent RNA helicase 1092 putative protein 1093 putative HMG protein 1094 squalene monooxygenase 2 (squalene epoxidase 2) (SE 2) (sp|O65403) 1095 eukaryotic peptide chain release factor subunit 1, putative 1096 auxin-induced protein-like 1097 putative lipoamide dehydrogenase 1098 putative protein 1099 unknown protein 1100 putative oligopeptide transporter 1101 putative translation elongation factor is 1102 putative CCAAT-binding transcription factor subunit 1103 putative ABC transporter 1104 putative superoxide-generating NADPH oxidase flavocytochrome 1105 aspartate kinase-homoserine dehydrogenase-like protein 1106 putative bHLH transcription factor 1107 putative geranylgeranyl transferase type I beta subunit 1108 putative ARP2/3 protein complex subunit p41 1109 sulphite reductase 1110 putative auxin-regulated protein 1111 transcription factor scarecrow-like 14, putative 1112 unknown protein 1113 monooxygenase 2 (MO2) 1114 putative amine oxidase 1115 zinc finger protein, putative 1116 DNA-binding protein, putative 1117 putative protein 1118 putative protein 1119 Avr9 elicitor response like protein 1120 putative protein 1121 hypothetical protein 1122 putative nucleotide-sugar dehydratase 1123 UFD1 like protein 1124 putative transprenyltransferase 1125 outward rectifying potassium channel KCO 1126 unknown protein 1127 putative pectinacetylesterase 1128 putative protein 1129 No function assigned by TIGR 1130 unknown protein 1131 unknown protein 1132 unknown protein 1133 protein phosphatase homolog (PPH1) 1134 unknown protein 1135 No function assigned by TIGR 1136 unknown protein 1137 unknown protein 1138 unknown protein 1139 putative protein 1140 unknown protein 1141 putative ubiquinol-cytochrome-c reductase 1142 unknown protein 1143 contains similarity to high- glucose-regulated protein 8 GB: AAF08813 GI: 6449083 from [Homo sapiens] 1144 unknown protein 1145 putative cis-Golgi SNARE protein 1146 unknown protein 1147 glutamate-1-semialdehyde aminotransferase 1148 No function assigned by TIGR 1149 hypothetical protein 1150 unknown protein 1151 unknown protein 1152 unknown protein 1153 scarecrow-like 3 1154 putative proline-rich protein 1155 cytochrome c oxidoreductase like protein 1156 putative carboxymethylenebutenolidase 1157 unknown protein 1158 unknown protein 1159 unknown protein 1160 unknown protein 1161 unknown protein 1162 unknown protein 1163 auxin-induced protein (IAA20) 1164 50S ribosomal protein L4 1165 putative DNA topoisomerase III beta 1166 No function assigned by TIGR 1167 isp4 like protein 1168 putative protein kinase 1169 hypothetical protein 1170 putative pyrophosphate-fructose- 6-phosphate 1-phosphotransferase 1171 putative protein 1172 putative protein 1173 putative protein 1174 unknown protein 1175 unknown protein 1176 putative protein 1177 putative protein 1178 unknown protein 1179 unknown protein 1180 putative protein 1181 brassinosteroid insensitive 1 gene (BRI1) 1182 putative receptor protein kinase 1183 vacuolar-type H+-translocating inorganic pyrophosphatase 1184 protein kinase-like protein 1185 glycyl tRNA synthetase, putative 1186 subtilisin proteinase-like 1187 hypothetical protein 1188 cytochrome P450-like protein 1189 cytochrome p450 like protein 1190 putative protein kinase 1191 pectinesterase-like protein 1192 putative receptor-like protein kinase 1193 peroxidase ATP17a-like protein 1194 No function assigned by TIGR 1195 cellulose synthase catalytic subunit-like protein 1196 RAS-related protein, RAB7 1197 putative aspartate aminotransferase 1198 cyclophilin 1199 putative SF2/ASF splicing modulator, Srp30 1200 putative cytochrome b5 1201 glutamyl-tRNA reductase, putative 1202 putative MADS-box protein 1203 ammonium transport protein (AMT1) 1204 No function assigned by TIGR 1205 putative beta-ketoacyl-CoA synthase 1206 thaumatin-like protein 1207 putative methionine aminopeptidase 1208 putative protein phosphatase 2C 1209 kinase-like protein 1210 receptor-associated kinase isolog 1211 mitochondrial ribosomal protein S14 1212 oleosin, 18.5K 1213 chalcone isomerase 1214 putative cyclin-dependent kinase regulatory subunit 1215 putative thaumatin-like protein 1216 putative two-component response regulator protein 1217 TATA binding protein associated factor, putative 1218 predicted protein of unknown function 1219 putative AP2 domain transcription factor 1220 brassinosteroid receptor kinase, putative 1221 TINY-like protein 1222 glucose-6-phosphate isomerase 1223 putative protein 1224 putative NAM (no apical meristem)-like protein 1225 unknown protein 1226 putative nucleotide-binding protein 1227 bZIP transcription factor (POSF21) 1228 ubiquitin activating enzyme-like protein 1229 telomere repeat-binding protein 1230 unknown protein 1231 mevalonate kinase 1232 putative protein 1233 hypothetical protein 1234 disease resistance RPP5 like protein 1235 putative protein 1236 putative pectinesterase 1237 Ttg1 protein (emb|CAB45372.1) 1238 FUSCA PROTEIN FUS6 1239 NHE1 Na+/H+ exchanger 1240 No function assigned by TIGR 1241 Phospholipase like protein 1242 unknown protein 1243 unknown protein 1244 unknown protein 1245 AUX1-like amino acid permease 1246 unknown protein 1247 putative C2H2-type zinc finger protein 1248 putative protein 1249 putative protein 1250 putative glucosyltransferase 1251 putative lipase 1252 putative protein 1253 putative thioredoxin 1254 AIG2-like protein 1255 short-chain alcohol dehydrogenase like protein 1256 hypothetical protein 1257 putative protein 1258 putative protein 1259 glutathione peroxidase- like protein 1260 putative protein 1261 putative disease resistance response protein 1262 putative protein 1263 senescence-associated protein (SAG29) 1264 glycolate oxidase, putative 1265 extensin-like protein 1266 putative protein 1267 unknown protein 1268 putative disease resistance protein 1269 putative receptor-like protein kinase 1270 putative receptor-like protein kinase 1271 basic chitinase 1272 putative pectin methylesterase 1273 peroxidase ATP N 1274 class 2 non-symbiotic hemoglobin 1275 nitrate transporter 1276 Ca2+/H+-exchanging protein-like 1277 putative protein 1278 hydroxynitrile lyase like protein 1279 putative AP2 domain transcription factor 1280 pectin methylesterase, putative 1281 putative protein 1282 beta-glucosidase-like protein 1283 CCAAT box binding factor/ transcription factor Hap2a 1284 putative fibrillin 1285 xyloglucan endo transglycosylase 1286 putative 10 kd chaperonin 1287 No function assigned by TIGR 1288 serine/threonine protein kinase ATPK10 1289 putative lipase 1290 choline kinase GmCK2p-like protein 1291 putative sugar transport protein, ERD6 1292 MYB27 protein-like 1293 DNA-binding protein, putative 1294 similar to cold acclimation protein WCOR413 [Triticum aestivum] 1295 unknown protein 1296 aquaporin (plasma membrane intrinsic protein 2B) 1297 No function assigned by TIGR 1298 P-Protein-like protein 1299 No function assigned by TIGR 1300 putative cytochrome P450 monooxygenase 1301 putative cytochrome P450 monooxygenase 1302 putative thioredoxin 1303 stromal ascorbate peroxidase 1304 ethylene responsive element binding factor-like protein (AtERF6) 1305 auxin transport protein EIR1 (gb|AAC39513.1) 1306 putative CONSTANS-like B-box zinc finger protein 1307 putative protein kinase 1308 mitochondrial Lon protease homolog 1 precursor (sp|O64948) 1309 putative protein 1310 heme activated protein, putative 1311 putative cytochrome P450 1312 No function assigned by TIGR 1313 putative lipase 1314 putative protein 1315 putative sugar transporter protein 1316 putative sucrose transport protein, SUC2 1317 putative protein 1318 putative protein 1319 putative endochitinase 1320 putative acetone- cyanohydrin lyase 1321 putative protein 1322 calmodulin-like protein 1323 hypothetical protein 1324 cysteine proteinase like protein 1325 heat shock protein 17.6-II 1326 heat shock protein 18 1327 Arabidopsis mitochondrion- localized small heat shock protein (AtHSP23.6-mito) 1328 unknown protein 1329 putative WRKY-type DNA binding protein 1330 No function assigned by TIGR 1331 hypothetical protein 1332 putative integral membrane protein nodulin 1333 putative protein 1334 unknown protein 1335 3-isopropylmalate dehydratase, small subunit 1336 unknown protein 1337 putative homeodomain transcription factor 1338 unknown protein 1339 putative protein 1340 peroxidase ATP19a 1341 putative Na+/H+ exchanging protein 1342 putative auxin-regulated protein 1343 unknown protein 1344 unknown protein 1345 putative trehalose-6- phosphate synthase 1346 putative lectin 1347 Mlo protein-like 1348 unknown protein 1349 ethylene response factor, putative 1350 unknown protein 1351 unknown protein 1352 bZIP transcription factor- like protein 1353 Medicago nodulin N21-like protein 1354 putative endo-1,4-beta glucanase 1355 1-aminocyclopropane-1- carboxylate oxidase 1356 putative anion exchange protein 1357 SRG1-like protein 1358 putative protein 1359 putative phi-1-like phosphate induced protein 1360 putative protein 1361 putative embryo-abundant protein 1362 putative hydrolase 1363 unknown protein 1364 unknown protein 1365 hexose transporter-like protein 1366 unknown protein 1367 unknown protein 1368 peptide transport-like protein 1369 unknown protein 1370 putative peptide transporter 1371 disease resistance protein, putative 1372 cysteine protease component of protease-inhibitor complex 1373 putative cytochrome P450 1374 putative protein 1375 hypothetical protein 1376 unknown protein 1377 putative phosphoribosylaminoimidazolecarboxamide formyltransferase 1378 putative protein 1379 HSP like protein 1380 unknown protein 1381 unknown protein 1382 putative cytochrome P450 1383 similar to pectinesterase 1384 putative glucosyltransferase 1385 thaumatin-like protein 1386 drought-inducible cysteine proteinase RD19A precursor 1387 vegetative storage protein Vsp2 1388 unknown protein 1389 unknown protein 1390 anthranilate N- benzoyltransferase-like protein 1391 delta-1-pyrroline 5- carboxylase synthetase (P5C1) 1392 glutathione S-conjugate transporting ATPase (AtMRP1) 1393 hypothetical protein 1394 hypothetical protein 1395 unknown protein 1396 putative protein 1397 putative protein 1398 No function assigned by TIGR 1399 unknown protein 1400 putative protein kinase 1401 unknown protein 1402 hypothetical protein 1403 unknown protein 1404 putative calcium-binding EF-hand protein 1405 cinnamyl-alcohol dehydrogenase ELI3-1 1406 putative protein 1407 unknown protein 1408 senescence-associated protein sen1 1409 hypothetical protein 1410 putative cytochrome P450 1411 proline oxidase, mitochondrial precursor (osmotic stress-induced proline dehydrogenase) 1412 putative response regulator 3 1413 hypothetical protein 1414 glutamine-dependent asparagine synthetase 1415 lysine-ketoglutarate reductase/saccharopine 1416 En/Spm-like transposon protein 1417 G-box binding bZIP transcription factor 1418 putative protein 1419 putative protein 1420 putative protein 1421 ATFP4-like 1422 unknown protein 1423 unknown protein 1424 putative protein 1425 invertase inhibitor homolog (emb|CAA73335.1) 1426 unknown protein 1427 unknown protein 1428 putative cytochrome b5 1429 putative protein 1430 putative protein 1431 putative protein 1432 No function assigned by TIGR 1433 putative copper/zinc superoxide dismutase 1434 protein phosphatase ABI1 1435 glutamate dehydrogenase 2 1436 No function assigned by TIGR 1437 low-temperature-induced protein 78 (sp|Q06738) 1438 putative myo-inositol 1-phosphate synthase 1439 phosphate transporter (gb|AAB17265.1) 1440 4-hydroxyphenylpyruvate dioxygenase (HPD) 1441 histone HI 1442 hypothetical protein 1443 No function assigned by TIGR 1444 neoxanthin cleavage enzyme-like protein 1445 dehydration-induced protein RD22 1446 zinc finger protein ZAT7 1447 unknown protein 1448 unknown protein 1449 unknown protein 1450 unknown protein 1451 putative protein 1452 putative protein 1453 RNA helicase, putative 1454 putative glycine-rich protein 1455 hypothetical protein 1456 putative protein 1457 peroxidase 1458 peroxidase ATP3a (emb|CAA67340.1) 1459 metallothionein-like protein 1460 endomembrane-associated Protein 1461 ferritin 1 precursor 1462 dehydrin RAB18-like protein (sp|P30185) 1463 HSR201 like protein 1464 light regulated protein, putative 1465 Dr4(protease inhibitor) 1466 mitogen activated protein kinase kinase (nMAPKK) 1467 glutathione S-transferase 1468 transcriptional activator CBF1/CRT/CRE binding factor 1 1469 homeobox-leucine zipper protein ATHB-12 1470 amino acid permease I 1471 MAP kinase (ATMPK7) 1472 potassium channel protein AKT3 1473 cytochrome P450 monooxygenase (CYP91A2) 1474 putative transport protein 1475 putative protein 1476 hypothetical protein 1477 putative protein 1478 hypothetical protein 1479 receptor protein kinase-like protein 1480 serine/threonine protein kinase-like protein 1481 putative auxin-regulated protein 1482 amino acid transport protein AAP2 1483 unknown protein 1484 cold and ABA inducible protein kinl 1485 gamma-VPE (vacuolar processing enzyme) 1486 putative protein 1 photosystem II oxygen-evolving complex 1487 myrosinase-associated protein, putative 1488 transcription factor ATMYB4 1489 H-protein promoter binding factor- 2a 1490 ammonium transporter, puitative 1491 putative zeta-carotene desaturase precursor 1492 high-affinity nitrate transporter NRT2 1493 light induced protein like 1494 putative AT-hook DNA-binding protein 1495 putative glycogenin 1496 putative light repressible receptor protein kinase 1497 serine/threonine kinase-like protein 1498 putative peroxidase 1499 cytochrome P450 monooxygenase (CYP83A1) 1500 MYB-related transcription factor (CCA1) 1501 Terminal flower1 (TFL1) 1502 sulfate transporter ATST1 1503 RING-H2 finger protein RHA3b 1504 lipoxygenase, putative 1505 serine 0-acetyltransferase (EC 2.3.1.30) Sat-52 (pir||S71207) 1506 ferulate-5-hydroxylase (FAH1) 1507 En/Spm-like transposon protein, putative 1508 calmodulin-binding-like protein 1509 hypothetical protein 1510 somatic embryogenesis receptor- like kinase-like protein 1511 putative giberellin beta- hydroxylase 1512 putative pectinesterase 1513 putative protein 1514 unknown protein 1515 ribosomal protein 1516 low-temperature-induced 65 kD protein (sp|Q04980) 1517 putative glucosyltransferase 1518 peroxidase (emb|CAA67551.1) 1519 ankyrin-like protein 1520 ribosomal protein S11-like 1521 hypothetical protein 1522 glycoprotein(EP1), putative 1523 calnexin-like protein 1524 SRG1-like protein 1525 ethylene response factor 1 (ERF1) 1526 transcriptional activator CBF1-like protein 1527 xyloglucan endo-1,4-beta D-glucanase (XTR-6) 1528 putative cinnamyl alcohol dehydrogenase 1529 gibberellin 3 beta- hydroxylase, putative 1530 auxin response transcription factor 3 (ETTIN/ARF3) 1531 No function assigned by TIGR 1532 putative protein 1533 similar to avrRpt2-induced protein 1 1534 unknown protein 1535 hypothetical protein 1536 putative protein kinase 1537 respiratory burst oxidase- like protein 1538 glucose-6- phosphate/phosphate- translocator precursor, putative 1539 class 1 non-symbiotic hemoglobin (AHB1) 1540 endochitinase isolog 1541 putative cytochrome P450 1542 60S acidic ribosomal protein P0 1543 putative protein 1544 auxin-induced protein, putative 1545 unknown protein 1546 hypothetical protein 1547 protein phosphatase 2C ABI2 (PP2C) (sp|O04719) 1548 peroxidase, prxr2 1549 putative peroxidase ATP12a 1550 putative beta-amylase 1551 putative acetone-cyanohydrin lyase 1552 fatty acid elongase 3-ketoacyl-CoA synthase 1 1553 putative citrate synthase 1554 pEARLI 1-like protein 1555 putative MYB family transcription factor 1556 putative transcription factor MYB28 1557 RNA helicase-like protein 1558 snoRNA 1559 putative protein kinase 1560 growth regulator like protein 1561 putative potassium transporter 1562 putative protein 1563 60S ribosomal protein L14 1564 unknown protein 1565 putative RING-H2 zinc finger protein 1566 putative pollen surface protein 1567 unknown protein 1568 unknown protein 1569 unknown protein 1570 putative Ca2+-ATPase 1571 1-aminocyclopropane-1- carboxylate synthase-like protein 1572 putative beta-glucosidase 1573 transcription factor ZAP1 1574 oligopeptide transporter, putative 1575 putative protein 1576 putative glucosyltransferase 1577 putative serine/threonine kinase 1578 squalene epoxidase-like protein 1579 similar to 14 KD proline-rich protein DC2.15 precursor (sp|P14009); similar to ESTs emb|Z17709 and emb|Z47685 1580 unknown protein 1581 unknown protein 1582 hypothetical protein 1583 60S ribosomal protein L38 1584 flavin-containing monooxygenase, putative 1585 remorin 1586 unknown protein 1587 putative protein 1588 lipoxygenase 1589 cold-regulated protein COR6.6 (KIN2) 1590 Myb transcription factor homolog (ATR1) 1591 putative protein 1592 unknown protein 1593 unknown protein 1594 Ca2+-transporting ATPase- like protein 1595 protein phosphatase 2C (AtP2C-HA) 1596 peroxidase ATP24a 1597 branched-chain alpha keto- acid dehydrogenase, putative 1598 putative beta-ketoacyl-CoA synthase 1599 putative protein 1600 putative beta-galactosidase 1601 putative protein 1602 60S ribosomal protein L27 1603 putative annexin 1604 NAC domain protein, putative 1605 unknown protein 1606 late embryogenesis abundant protein LEA like 1607 unknown protein 1608 putative protein 1609 dehydrin Xero2 1610 putative zinc finger protein 1611 unknown protein 1612 DnaJ-like protein 1613 putative inositol polyphosphate-5- phosphatase- 1614 putative cytochrome P450 1615 putative protein 1616 unknown protein 1617 putative protein 1618 hypothetical protein 1619 putative protein 1620 sucrose-UDP glucosyltransferase 1621 glucose-6-phosphate 1- dehydrogenase 1622 unknown protein 1623 mitochondria chaperonin (HSP60) 1624 sucrose transport protein SUC1 1625 putative protein disulfide isomerase 1626 putative pollen-specific protein 1627 integral membrane protein, putative 1628 rubredoxin, putative 1629 putative protein 1630 disease resistance protein RPS4, putative 1631 putative peptide/amino acid Transporter 1632 peroxidase, putative 1633 ethylene receptor, putative (ETR2) 1634 protein phosphatase 2C (PP2C) 1635 putative glutathione 5-transferase 1636 homeodomain transcription factor (ATHB-7) 1637 putative nitrate transporter 1638 putative ribosomal protein L9, cytosolic 1639 putative DNA-binding protein 1640 beta-1,3-glucanase-like protein 1641 putative zinc transporter 1642 transcription factor TINY 1643 putative aspartate kinase- homoserine dehydrogenase 1644 ethylene reponse factor-like AP2 domain transcription factor 1645 peptide transporter-like protein 1646 trehalose-6-phosphate synthase like protein 1647 putative ribonuclease 1648 hypothetical protein 1649 putative DNA-binding protein 1650 nodulin-like protein 1651 trehalose-6-phosphate phosphatase-like protein 1652 succinate dehydrogenase flavoprotein alpha subunit (emb|CAA05025.1) 1653 unknown protein 1654 stress related protein, putative 1655 putative chloroplast initiation factor 3 1656 putative protein 1657 hypothetical protein 1658 putative CCCH-type zinc finger protein 1659 similar to harpin-induced protein hin 1 from tobacco 1660 unknown protein 1661 unknown protein 1662 hypothetical protein 1663 No function assigned by TIGR 1664 putative protein 1665 putative glutathione S transferase TSI-1 1666 putative protein 1667 putative PTR2 family peptide transporter 1668 receptor kinase-like protein 1669 putative sugar transport protein, ERD6 1670 putative protein 1671 nodulin-like protein 1672 unknown protein 1673 putative receptor-like protein kinase 1674 glutathione-conjugate transporter AtMRP4 1675 ascorbate oxidase-like protein 1676 pathogenesis-related protein 1 precursor, 19.3K 1677 R2R3-MYB transcription factor 1678 hypothetical protein 1679 putative chitinase 1680 Mlo protein, putative 1681 putative WRKY-type DNA binding protein 1682 putative acyl-CoA synthetase 1683 putative pathogenesis-related protein 1684 putative chitinase 1685 germin precursor oxalate oxidase 1686 endoxyloglucan transferase, putative 1687 putative protein 1688 putative cytochrome P450 1689 similar to Mlo proteins from H. vulgare 1690 putative tropinone reductase 1691 extensin-like protein 1692 putative sarcosine oxidase 1693 putative protein 1694 hypothetical protein 1695 late embryogenesis-abundant protein, putative 1696 beta-carotene hydroxylase 1697 putative calcium binding protein 1698 unknown protein 1699 unknown protein 1700 predicted glycosyl transferase 1701 hypothetical protein 1702 hypothetical protein 1703 hypothetical protein 1704 putative protein 1705 unknown protein 1706 putative protein 1707 putative protein 1708 serine/threonine kinase-like protein 1709 No function assigned by TIGR 1710 putative pectinesterase 1711 peroxidase like protein 1712 No function assigned by TIGR 1713 phenylalanine ammonia lyase (PAL1) 1714 peroxidase (emb|CAA68212.1) 1715 putative AMP deaminase 1716 putative MYB family transcription factor 1717 DNA-directed RNA polymerase II, third largest subunit 1718 nucleotide pyrophosphatase- like protein 1719 putative peroxidase 1720 calcium sensor homolog (gb|AAC26110.1) 1721 putative GDSL-motif lipase/hydrolase 1722 putative nonspecific lipid- transfer protein 1723 acyl-carrier protein (ACP), putative 1724 putative glycine dehydrogenase 1725 AIG1 1726 ACC synthase (AtACS-6) 1727 cyclin delta-3 1728 putative RING zinc finger protein 1729 aldose 1-epimerase-like protein 1730 putative phospholipase 1731 phosphoenolpyruvate carboxylase 1732 putative galactinol synthase 1733 unknown protein 1734 putative protein 1735 1-aminocyclopropane-1- carboxylate oxidase 1736 thioredoxin (clone GIF1) (pir||S58118) 1737 trehalose-6-phosphate phosphatase 1738 beta-1,3-glucanase 2 (BG2) (PR-2) 1739 putative S-adenosyl-L- methionine:trans-caffeoyl- Coenzyme A 3-O- methyltransferase 1740 disease resistance protein EDS1 1741 putative protein kinase 1742 Gluthatione reductase, chloroplast precursor 1743 putative heat shock protein 1744 aspartate kinase 1745 putative major intrinsic (channel) protein 1746 matrix metalloproteinase, putative 1747 putative GDSL-motif lipase/hydrolase 1748 putative protein 1749 DAG-like protein 1750 serine/threonine kinase-like protein 1751 formamidase-like protein 1752 CER2 1753 26S proteasome subunit 4 1754 pectinesterase like protein 1755 putative disease resistance protein 1756 putative RNA methyltransferase 1757 unknown protein 1758 HOMEOBOX PROTEIN KNOTTED-1 LIKE 4 (KNAT4) 1759 glycine-rich RNA-binding protein AtGRP2-like 1760 putative acetylornithine transaminase 1761 putative Sec24-like COPII protein 1762 putative berberine bridge enzyme 1763 putative GH3-like protein 1764 putative ABC transporter 1765 putative reticuline oxidase-like protein 1766 pectate lyase-like protein 1767 protein disulfide-isomerase-like protein 1768 putative protein 1769 putative membrane transporter 1770 unknown protein 1771 unknown protein 1772 putative RING-H2 zinc finger protein 1773 unknown protein 1774 unknown protein 1775 unknown protein 1776 MADS-box protein (AGL20) 1777 amidophosphoribosyltransferase 2 precursor 1778 putative dihydrodipicolinate synthase 1779 hypothetical protein 1780 ABA-responsive protein- like 1781 putative protein 1782 hypothetical protein 1783 DNA-binding protein-like 1784 No function assigned by TIGR 1785 transcription factor, putative 1786 nitrate reductase, putative 1787 putative protein 1788 putative protein 1789 putative protein 1790 putative protein 1791 unknown protein 1792 unknown protein 1793 tryptophan synthase beta- subunit (TSB2) 1794 hypothetical protein 1795 putative protein 1796 putative DNA-binding protein 1797 putative 40S ribosomal protein S10 1798 putative protein 1799 putative cytochrome P450 1800 putative protein 1801 putative protein 1802 putative glucosyltransferase 1803 No function assigned by TIGR 1804 putative protein 1805 putative protein 1806 unknown protein 1807 glycine-rich RNA binding protein 7 1808 dehydrin, putative 1809 putative endoxyloglucan glycosyltransferase 1810 glutamate decarboxylase 1 (GAD 1) (sp|Q42521) 1811 delta 9 desaturase 1812 UDP-glucose glucosyltransferase 1813 CARBONIC ANHYDRASE 2 1814 response reactor 2 (ATRR2) 1815 S-adenosyl-methionine-sterol-C- methyltransferase, putative 1816 putative DNA-binding protein (RAV2-like) 1817 gamma glutamyl hydrolase, putative 1818 protein phosphatase-like 1819 unknown protein 1820 unknown protein 1821 unknown protein 1822 copper transport protein-like protein 1823 hypothetical protein 1824 unknown protein 1825 putative peptide methionine sulfoxide reductase 1826 putative obtusifoliol 14-alpha demethylase 1827 glutamate dehydrogenase (EC 1.4.1.—) 1 (pir||S71217) 1828 unknown protein 1829 xyloglucan endo-1,4-beta-D- glucanase precursor 1830 unknown protein 1831 SNF1 related protein kinase (ATSRPK1) 1832 putative protein 1833 putative chloroplast nucleoid DNA binding protein 1834 hypothetical protein 1835 putative protein 1836 putative thiamin biosynthesis protein 1837 unknown protein 1838 unknown protein 1839 putative RNA helicase 1840 putative SF21 protein {Helianthus annuus} 1841 unknown protein 1842 NBS/LRR disease resistance protein, putative 1843 hypothetical protein 1844 unknown protein 1845 No function assigned by TIGR 1846 glycine-rich protein (AtGRP2) 1847 No function assigned by TIGR 1848 putative protein 1849 putative glucosyltransferase 1850 hypothetical protein 1851 hypothetical protein 1852 putative protein 1853 putative disease resistance protein 1854 thaumatin, putative 1855 putative proline-rich protein 1856 sterol-C-methyltransferase 1857 superoxidase dismutase 1858 TINY-like protein 1859 calcium-dependent protein kinase, putative 1860 hypothetical protein 1861 putative protein kinase 1862 DNA-directed RNA polymerase (mitochondrial) 1863 putaive DNA-binding protein 1864 late embryogenesis abundant M17 protein 1865 putative protein 1866 delta-1-pyrroline-5- carboxylate synthetase 1867 putative 60s ribosomal protein L10 1868 cytochrome P450 CYP86A1 1869 putative tyrosine aminotransferase 1870 thionin 1871 No function assigned by TIGR 1872 APETALA2 protein 1873 MADS-box protein (AGL3) 1874 putative monooxygenase 1875 ZFP3 zinc finger protein 1876 cell division protein FtsZ chloroplast homolog precursor (sp|Q42545) 1877 calreticulin, putative 1878 phosphoserine aminotransferase 1879 12-oxophytodienoate-10,11- reductase 1880 putative bHLH transcription factor 1881 pectin methylesterase (PMEU1), putative 1882 DNA-binding protein 1883 carnitine racemase like protein 1884 putative protein 1885 endoxyloglucan transferase (dbj|BAA81669.1) 1886 RMA1 RING zinc finger protein 1887 ammonium transporter 1888 apyrase (gb|AAF00612.1) 1889 potassium uptake transporter-like protein 1890 putative ABC transporter 1891 potassium transporter-like protein 1892 integral membrane protein, putative 1893 putative protein 1894 pyruvate decarboxylase-1 (Pdc 1) 1895 putative malate oxidoreductase 1896 putative histone H2B 1897 snoRNA 1898 symbiosis-related like protein 1899 unknown protein 1900 unknown protein 1901 hypothetical protein 1902 putative protein 1903 copper-binding protein-like 1904 putative protein 1905 unknown protein 1906 putative glyoxalase II 1907 No function assigned by TIGR 1908 hypothetical protein 1909 flavanone 3-hydroxylase (FH3) 1910 putative laccase 1911 putative protein kinase 1912 myb-related protein, 33.3K (pir||S71284) 1913 unknown protein 1914 endo-xyloglucan transferase- like protein 1915 TMV resistance protein N- like 1916 putative xyloglucan endotransglycosylase 1917 unknown protein 1918 proline transporter 2 1919 resistance protein, putative 1920 actin, putative 1921 putative related to microbial divalent cation tolerance proteins 1922 unknown protein 1923 putative glycosyl transferase 1924 unknown protein 1925 putative protein phosphatase 2C 1926 unknown protein 1927 serpin, putative 1928 cinnamyl-alcohol dehydrogenase CAD1 1929 putative protein import receptor 1930 unknown protein 1931 unknown protein 1932 putative protein 1933 putative CDP- diacylglycerol-glycerol-3- phosphate 3- phosphatidyltransferase 1934 unknown protein 1935 putative LRR receptor-like protein kinase 1936 serine/threonine protein kinase, putative 1937 potassium transporter-like protein 1938 lactate dehydrogenase (LDH1) 1939 hypothetical protein 1940 unknown protein 1941 putative thaumatin 1942 putative reticuline oxidase-like protein 1943 uracil phosphoribosyltransferase, putative 1944 transcription factor, putative 1945 unknown protein 1946 unknown protein 1947 GATA transcription factor 4 1948 unknown protein 1949 unknown protein 1950 senescence-associated protein-like 1951 putative pollen allergen 1952 unknown protein 1953 putative protein 1954 glycine-rich protein 1955 putative protein 1956 3-methyladenine DNA glycosylase, putative 1957 endoplasmic reticulum-type calcium- transporting ATPase 4 1958 putative pectinesterase 1959 cytochrome P450-like protein 1960 RNA-binding protein (cp33) 1961 CONSTANS-like 1 1962 putative small heat shock protein 1963 hypothetical protein 1964 unknown protein 1965 cytochrome P450-like protein 1966 cysteine proteinase inhibitor like protein 1967 nicotianamine synthase (dbj|BAA74589.1) 1968 copper amine oxidase like protein (fragment2) 1969 putative SCARECROW gene regulator 1970 unknown protein 1971 unknown protein 1972 putative alanine acetyl transferase 1973 unknown protein 1974 unknown protein 1975 unknown protein 1976 putative extensin 1977 putative protein kinase 1978 putative protein kinase 1979 NADPH-dependent codeinone reductase, putative 1980 peroxidase 1981 putative cytochrome P450 1982 No function assigned by TIGR 1983 putative zinc-finger protein (B-box zinc finger domain) 1984 putative tyrosine aminotransferase 1985 hypothetical protein 1986 DNA binding protein 1987 putative fatty acid elongase 1988 bZIP transcription factor- like protein 1989 xyloglucan fucosyltransferase, putative 1990 unknown protein 1991 unknown protein 1992 putative protein 1993 myb factor, putative 1994 Myb-family transcription factor, putative 1995 putative fructose bisphosphate aldolase 1996 myrosinase-associated protein, putative 1997 cytochrome P450 like protein 1998 similar to SOR1 from the fungus Cercospora nicotianae 1999 similar to embryo- abundant protein GB: L47672 GI: 1350530 from [Picea glauca] 2000 alcohol dehydrogenase 2001 auxin response factor 1 2002 pathogenesis-related protein 1 precursor, 18.9K 2003 hypothetical protein. 2004 unknown protein 2005 zinc finger protein Zat12 2006 unknown protein 2007 unknown protein 2008 cyclin, putative 2009 2-dehydro-3- deoxyphosphoheptonate aldolase 2010 glutathione synthetase gsh2 2011 heat shock protein 17 2012 putative Na+-dependent inorganic phosphate cotransporter 2013 No function assigned by TIGR 2014 unknown protein 2015 putative protein 2016 similar to RING-H2 finger protein RHC1a GB: AAC69854 GI: 3790583 from [Arabidopsis thaliana] 2017 calcium-binding protein-like 2018 putative protein 2019 putative aldehyde dehydrogenase 2020 auxin-responsive GH3-like protein 2021 putative protein 2022 Phosphoglycerate dehydrogenase- like protein 2023 unknown protein 2024 unknown protein 2025 PSI type III chlorophyll a/b- binding protein, putative 2026 putative protein 2027 putative protein 2028 glutaredoxin, putative 2029 hypothetical protein 2030 No function assigned by TIGR 2031 putative protein 2032 jasmonate inducible protein, putative 2033 putative polygalacuronase isoenzyme 1 beta subunit 2034 putative small heat shock protein 2035 unknown protein 2036 putative disease resistance protein 2037 putative protein 2038 ethylene-responsive element binding factor, putative 2039 putative protein 2040 Pollen-specific protein precursor like 2041 putative protein 2042 unknown protein 2043 EF-Hand containing protein- like 2044 unknown protein 2045 puative calcium transporting ATPase 2046 antifungal protein-like (PDF1.2) 2047 pathogenesis-related PR-1- like protein 2048 similar to Mlo proteins from H. vulgare 2049 putative steroid sulfotransferase 2050 trehalase-like protein 2051 thioredoxin fl 2052 unknown protein 2053 alanine-glyoxylate aminotransferase 2054 integral membrane protein, putative 2055 hypothetical protein 2056 unknown protein 2057 hypothetical protein 2058 unknown protein 2059 unknown protein 2060 unknown protein 2061 drought-induced-19-like 1 2062 unknown protein 2063 putative protein 2064 putative protein 2065 AIG2-like protein 2066 Lhca2 protein 2067 phytocyanin 2068 putative chlorophyll A-B binding protein 2069 Lhcb3 chlorophyll a/b binding protein (gb|AAD28773.1) 2070 luminal binding protein (dbj|BAA13948.1) 2071 hydroxypyruvate reductase (HPR) 2072 epoxide hydrolase (ATsEH) 2073 putative protein (fragment) 2074 unknown protein 2075 hypothetical protein 2076 putative glucosyl transferase 2077 putative glucosyl transferase 2078 putative 3-methylcrotonyl-CoA carboxylase 2079 putative peroxidase 2080 acyl-CoA oxidase (gb|AAC13497.1) 2081 alternative oxidase 1a precursor 2082 putative transcription factor (MYB4) 2083 serine acetyltransferase 2084 ATP-sulfurylase 2085 calreticulin (crtl) 2086 putative prohibitin 2 2087 putative monodehydroascorbate reductase 2088 branched-chain alpha-keto acid decarboxylase El beta subunit 2089 cytokinin oxidase-like protein 2090 putative receptor-like protein kinase 2091 unknown protein 2092 hypothetical protein 2093 No function assigned by TIGR 2094 putative APG protein 2095 glutathione S-transferase, putative 2096 phytochrome-associated protein 1 (PAP1) 2097 amidophosphoribosyltransferase 2098 nonphototropic hypocotyl 1 2099 3-keto-acyl-CoA thiolase 2 (gb|AAC17877.1) 2100 pEARLI 1 2101 glutathione reductase, cytosolic 2102 putative protein 2103 putative protein 2104 putative aldehyde oxidase 2105 probable photosystem I chain XI precursor 2106 photosystem II polypeptide, putative 2107 photosystem II reaction center 6.1 KD protein 2108 33 kDa polypeptide of oxygen-evolving complex (OEC) in photosystem II (emb|CAA75629.1) 2109 60S ribosomal protein L11B 2110 extA (emb|CAA47807.1) 2111 zinc finger protein OBP4- like 2112 sterol delta7 reductase 2113 putative RAS-related protein, RAB11C 2114 glucosyltransferase like protein 2115 zinc finger protein (PMZ), putative 2116 6,7-dimethyl-8- ribityllumazine synthase precursor 2117 putative protein 2118 osmotin precursor 2119 No function assigned by TIGR 2120 ferredoxin precusor isolog 2121 GH3 like protein 2122 non-specific lipid transfer protein 2123 homeodomain transcription factor (HAT9) 2124 putative cytochrome P450 monooxygenase 2125 putative protein kinase 2126 putative protein 2127 glyceraldehyde-3- phosphate dehydrogenase 2128 putative protein disulfide- isomerase 2129 unknown protein 2130 beta-1,3-glucanase class I precursor 2131 homeobox-leucine zipper protein HAT5 (HD-ZIP protein 5) (HD- ZIP protein ATHB-1) 2132 putative cyclic nucleotide- regulated ion channel protein 2133 P II nitrogen sensing protein GLBI 2134 H-protein promoter binding factor 1 (gb|AAC24592.1) 2135 GASTI-like protein 2136 cytochrome P450 GA3 2137 putative protein 2138 Myb-related transcription factor- like protein 2139 putative phloem-specific lectin 2140 protein kinase-like protein 2141 unknown protein 2142 SCARECROW transcriptional regulator-like 2143 unknown protein 2144 unknown protein 2145 putative protein 2146 calnexin homolog 2147 PP1/PP2A phosphatases pleiotropic regulator PRL2 2148 xyloglucan endotransglycosylase, putative 2149 putative calmodulin 2150 spermine synthase (ACL5) 2151 snoRNA 2152 photosystem I subunit V precursor, putative 2153 putative potassium transporter 2154 Homeodomain-like protein 2155 putative protein 2156 unknown protein 2157 CALMODULIN-RELATED PROTEIN 2, TOUCH-INDUCED (TCH2) 2158 putative protein phosphatase 2C 2159 monosaccharide transport protein, STP4 2160 hypothetical protein 2161 unknown protein 2162 hypothetical protein 2163 putative protein kinase 2164 putative serine/threonine protein kinase 2165 jasmonate inducible protein, putative 2166 similar to several small proteins (~100aa) that are induced by heat, auxin, ethylene and wounding such as Phaseolus aureus indole-3-acetic acid induced protein ARG (SW: 32292) 2167 unknown protein 2168 MYB-like protein 2169 putative protein kinase 2170 unknown protein 2171 CLC-d chloride channel protein 2172 cytochrome P450-like protein 2173 putative glutathione S- transferase 2174 putative mandelonitrile lyase 2175 hypothetical protein 2176 putative trypsin inhibitor 2177 male sterility 2-like protein (emb|CAA68191.1) 2178 unknown protein 2179 unknown protein 2180 putative protein 2181 putative peroxidase 2182 putative thromboxane-A synthase 2183 putative cytochrome P450 2184 peroxidase ATP21a 2185 unknown protein 2186 putative glutathione S- transferase 2187 defender against cell death protein 2188 AP2 domain containing protein, putative 2189 actin depolymerizing factor-like protein 2190 putative calcium-dependent protein kinase (U90439) 2191 phosphoribosylanthranilate transferase, putative 2192 oligopeptide transporter, putative 2193 calmodulin-like protein 2194 putative protease inhibitor 2195 MAP kinase 2196 DNA binding protein MybStl, putative 2197 putative protein 2198 putative protein 2199 unknown protein 2200 unknown protein 2201 unknown protein 2202 putative protein 2203 unknown protein 2204 unknown protein 2205 hypothetical protein 2206 uncharacterized protein 2207 putative protein 2208 hypothetical protein 2209 peroxidase (emb|CAA66967.1) 2210 putative flavonol 3-O- glucosyltransferase 2211 putative flavonol 3-O- glucosyltransferase 2212 putative protein 2213 glycerol-3-phosphate acyltransferase 2214 putative beta-1,3-glucanase 2215 putative ethylene response element binding protein (EREBP) 2216 putative CONSTANS-like B-box zinc finger protein 2217 putative protein 2218 unknown protein 2219 putative trehalose-6-phosphate phosphatase (AtTPPA) 2220 putative protein 2221 putative protein 2222 unknown protein 2223 unknown protein 2224 unknown protein 2225 hypothetical protein 2226 putative metal-binding protein 2227 putative phosphoribosylglycinamide synthetase 2228 unknown protein 2229 putative protein 2230 unknown protein 2231 unknown protein 2232 putative beta-galactosidase 2233 putative protein kinase 2234 putative protein 2235 putative protein phosphatase 2C 2236 putative growth regulator protein 2237 putative ABC transporter 2238 chloride channel (emb|CAA70310.1) 2239 adrenodoxin-like protein 2240 NAM (no apical meristem)- like protein 2241 putative transcription factor MYB41 2242 Myb DNA binding protein- like 2243 AtMYB84 2244 photosystem II type I chlorophyll a/b binding protein 2245 putative aspartic proteinase 2246 jasmonate inducible protein, putative 2247 putative protein 2248 No function assigned by TIGR 2249 putative phosphatidylserine synthase 2250 putative nicotianamine synthase 2251 lysine and histidine specific transporter, putative 2252 putative protein 2253 putative protein 2254 putative sugar transporter protein 2255 12S cruciferin seed storage protein 2256 putative auxin-induced protein, IAA17/AXR3-1 2257 putative cyclin D 2258 farnesyl diphosphate synthase precursor (gb|AAB49290.1) 2259 putative potassium transport protein (TRH1) 2260 putative NPK1-related MAP kinase 2261 putative protein 2262 putative ABC transporter 2263 putative DNA-directed RNA polymerase subunit 2264 putative small nuclear ribonucleoprotein E 2265 unknown protein 2266 reticuline oxidase-like protein 2267 putative 1-aminocyclopropane-1- carboxylate oxidase 2268 similar to Mlo proteins from H. vulgare 2269 long-chain-fatty-acid-CoA ligase- like protein 2270 putative protein 2271 chromatin remodelling complex ATPase chain ISWI-like protein 2272 hypothetical protein 2273 latex-abundant protein, putative 2274 N-acetylornithine deacetylase-like protein, fragment 2275 putative DNA-binding protein 2276 putative anthranilate N- hydroxycinnamoyl/lbenzoyltransferase 2277 putative DNA binding protein 2278 cytochrome P450-like protein 2279 putative DNA-binding protein 2280 putative peptide transporter 2281 putative reticuline oxidase-like protein 2282 thioredoxin, putative 2283 nodulin-like protein 2284 UDP-galactose transporter- like protein 2285 putative fibrillin 2286 unknown protein 2287 unknown protein 2288 unknown protein 2289 hypothetical protein 2290 glyceraldehyde 3-phosphate dehydrogenase A subunit (GapA) 2291 predicted protein of unknown function 2292 putative protein 2293 putative protein 2294 myb-like protein 2295 hypothetical protein 2296 putative U5 small nuclear ribonucleoprotein, an RNA helicase 2297 unknown protein 2298 cinnamyl alcohol dehydrogenase-like protein 2299 hypothetical protein similar to extensin-like protein 2300 unknown protein 2301 putative chlorophyll a/b binding protein 2302 probable plasma membrane intrinsic protein 1c 2303 hexokinase (ATHXK2) 2304 calcium-dependent protein kinase 2305 5′-adenylylphosphosulfate reductase, putative 2306 Erd1 protein precursor (sp|P42762) 2307 putative protein 2308 putative protein 2309 unknown protein 2310 BCS1 protein-like protein 2311 putative protein 2312 putative protein 2313 putative protein kinase 2314 indoleacetic acid (IAA)-inducible gene (IAA7) 2315 ATP-dependent Clp protease regulatory subunit CLPX 2316 DNA-binding protein RAV1 2317 putative protein 2318 hypothetical protein 2319 unknown protein 2320 unknown protein 2321 putative protein 2322 putative thioredoxin reductase 2323 unknown protein 2324 putative lectin 2325 No function assigned by TIGR 2326 beta-fructosidase 2327 chlorophyll a/b-binding protein CP29 2328 photosystem I subunit PSI-E-like protein 2329 peroxidase ATP8a 2330 putative fructose bisphosphate aldolase 2331 zinc finger protein ATZF1, putative 2332 DegP protease precursor 2333 transcription factor-like protein 2334 calcium-dependent protein kinase 2335 hypothetical protein 2336 putative protein 2337 glucose-1-phosphate adenylyltransferase (APL3) 2338 No function assigned by TIGR 2339 putative Eukaryotic initiation factor 4A 2340 No function assigned by TIGR 2341 unknown protein 2342 beta tubulin 1, putative 2343 one helix protein (OHP) 2344 No function assigned by TIGR 2345 zinc finger protein 5, ZFP5 2346 putative MYB family transcription factor 2347 putative amino acid transporter protein 2348 putative potassium transporter 2349 protein kinase (AFC2) 2350 putative protein 2351 No function assigned by TIGR 2352 putative ubiquitin- conjugating enzyme E2 2353 unknown protein 2354 cytochrome P450 monooxygenase (CYP7IB3) 2355 putative myrosinase binding protein 2356 putative vacuolar sorting receptor 2357 uridine diphosphate glucose epimerase 2358 shaggy related protein kinase, ASK-GAMMA 2359 ankyrin repeat protein EMB506 2360 putative beta-alanine pyruvate aminotransferase 2361 putative alcohol dehydrogenase 2362 putative receptor-like protein kinase 2363 unknown protein 2364 putative methylmalonate semi-aldehyde dehydrogenase 2365 hypothetical protein 2366 unknown protein 2367 peroxidase ATP13a 2368 putative glutathione peroxidase 2369 squamosa promoter binding protein-like 7 2370 photosystem II core complex protein, putative 2371 snoRNA 2372 photosystem I subunit X precursor 2373 MYB transcription factor (Atmyb2) 2374 putative PHD-type zinc finger protein 2375 nuclear RNA binding protein A- like protein 2376 unknown protein 2377 unknown protein 2378 unknown protein 2379 putative amino-cyclopropane- carboxylic acid oxidase (ACC oxidase) 2380 hypothetical protein 2381 indole-3-acetate beta glucosyltransferase like protein 2382 predicted protein 2383 unknown protein 2384 No function assigned by TIGR 2385 putative photosystem I reaction center subunit IV 2386 putative homeodomain transcription factor 2387 putative purple acid phosphatase precursor 2388 No function assigned by TIGR 2389 nitrate reductase 1(NR1) 2390 putative casein kinase II beta subunit 2391 pEARLI 1-like protein 2392 putative protein 2393 No function assigned by TIGR 2394 unknown protein 2395 putative cell wall-plasma membrane disconnecting CLCT protein (AIR1A) 2396 unknown protein 2397 scarecrow-like 11-like 2398 putative anthocyanidin synthase 2399 putative AP2 domain transcription factor 2400 caffeoyl-CoA O-methyltransferase- like protein 2401 unknown protein 2402 putative protein kinase 2403 cytochrome P450-like protein 2404 putative MADS-box protein ANR1 2405 putative glutathione S-transferase 2406 hypothetical protein 2407 similar to gibberellin- regulated proteins 2408 unknown protein 2409 putative sensory transduction histidine Kinase 2410 similar to late embryogenesis abundant proteins 2411 unknown protein 2412 putative protein 2413 putative ATP-dependent RNA helicase 2414 putative protein 2415 putative sucrose synthetase 2416 beta-fructofuranosidase 1 2417 putative indole-3-acetate beta-glucosyltransferase 2418 hypothetical protein 2419 DNA-directed RNA polymerase II, third largest subunit 2420 putative transcription factor 2421 homeobox-leucine zipper protein ATHB-5 (HD-zip protein ATHB-5) (sp|P46667) 2422 putative ftsH chloroplast protease 2423 replication protein A1-like 2424 hypothetical protein 2425 unknown protein 2426 unknown protein 2427 putative methionine aminopeptidase 2428 unknown protein 2429 fatty acid elongase-like protein (cer2-like) 2430 unknown protein 2431 putative disease resistance response protein 2432 putative protein 2433 unknown protein 2434 putative protein 2435 putative protein 2436 unknown protein 2437 putative protein 2438 unknown protein 2439 unknown protein 2440 putative protein 2441 No function assigned by TIGR 2442 MADS-box protein AGL14 2443 No function assigned by TIGR 2444 peptidylprolyl isomerase 2445 putative s-adenosylmethionine synthetase 2446 peroxidase 2447 ferrochelatase-I 2448 putative eukaryotic initiation factor 4, eIF4 2449 drought-inducible cysteine proteinase RD21A precursor-like protein 2450 unknown protein 2451 unknown protein 2452 No function assigned by TIGR 2453 No function assigned by TIGR 2454 salt-inducible like protein 2455 glucose-6-phosphate 1- Dehydrogenase 2456 3-hydroxy-3-methylglutaryl CoA reductase (AA 1-592) 2457 hypothetical protein 2458 putative protein 2459 putative putative 60S ribosomal protein L17 2460 putative inorganic pyrophosphatase 2461 putative gamma- glutamyltransferase 2462 heat shock transcription factor- like protein 2463 mitochondrial chaperonin hsp60 2464 unknown protein 2465 putative zinc finger protein identical to T10M13.22 2466 putative uridylyl transferase 2467 nodulin-like protein 2468 putative B-box zinc finger protein 2469 No function assigned by TIGR 2470 putative metalloproteinase 2471 putative cellular apoptosis susceptibility protein 2472 hypothetical protein 2473 hypothetical protein 2474 scarecrow-like 13 (SCL13) 2475 putative nucleoside triphosphatase 2476 unknown protein 2477 No function assigned by TIGR 2478 hypothetical protein 2479 putative phospholipase 2480 putative snRNP protein 2481 putative protein 2482 putative lipase 2483 putative nonsense-mediated mRNA decay protein 2484 No function assigned by TIGR 2485 protochlorophyllide reductase precursor 2486 No function assigned by TIGR 2487 trehalose-6-phosphate synthase, putative 2488 unknown protein 2489 germin-like protein 2490 plastid protein 2491 putative protein 2492 hypothetical protein 2493 unknown protein 2494 unknown protein 2495 histone deacetylase-like protein 2496 unknown protein 2497 unknown protein 2498 putative protein 2499 putative protein 2500 No function assigned by TIGR 2501 putative zinc transporter ZIP2-like 2502 unknown protein 2503 putative ribosomal-protein S6 kinase (ATPK19) 2504 unknown protein 2505 unknown protein 2506 60S ribosomal protein L10A 2507 putative protein 2508 receptor protein kinase (IRK1), putative 2509 putative nematode-resistance protein 2510 tubulin alpha-5 chain-like protein 2511 putative DNA-binding protein 2512 unknown protein 2513 putative RGA1, giberellin repsonse modulation protein 2514 non phototropic hypocotyl 1-like 2515 RING-H2 finger protein RHA1b 2516 putative myb-protein 2517 hydroperoxide lyase (HPOL) like protein 2518 serine/threonine-protein kinase, PK7 2519 putative vacuolar proton-ATPase subunit 2520 putative polygalacturonase 2521 putative ribosomal protein L8 2522 putative adenylate kinase 2523 germin-like protein (GLP10) 2524 putative chlorophyll a/b binding protein 2525 chloroplast single subunit DNA- dependent RNA polymerase 2526 putative protein 2527 hypothetical protein 2528 hypothetical protein 2529 b-keto acyl reductase, putative 2530 cellulose synthase catalytic subunit 2531 putative 1-aminocyclopropane-1- carboxylate oxidase 2532 S-linalool synthase, putative 2533 phosphoribosyl-ATP pyrophosphohydrolase (At-IE) 2534 disease resistance RPP5 like protein (fragment) 2535 putative protein 2536 beta-galactosidase like protein 2537 putative translation initiation factor eIF-2, gamma subunit 2538 ankyrin like protein 2539 histone H2A-like protein 2540 putative protein 2541 salt-tolerance zinc finger protein 2542 unknown protein 2543 putative protein 2544 fructose-bisphosphate aldolase 2545 peroxidase (emb|CAA66964.1) 2546 patatin-like protein 2547 salt-inducible protein homolog 2548 hypothetical protein 2549 xyloglucan endo- transglycosylase-like protein 2550 trihelix DNA-binding protein (GT2) 2551 ubiquitin-conjugating enzyme 16, putative 2552 homeobox protein 2553 envelope Ca2+-ATPase 2554 snap25a 2555 putative annexin 2556 putative protein 2557 homeodomain transcription factor (ATHB-14) 2558 heat shock protein, putative 2559 peroxidase ATP23a 2560 p68 RNA helicase, putative 2561 potassium transporter, putative 2562 putative eukaryotic translation initiation factor 2 alpha subunit, eIF2 2563 hypothetical protein 2564 carnitine racemase like protein 2565 No function assigned by TIGR 2566 unknown protein 2567 unknown protein 2568 unknown protein 2569 serine/threonine kinase-like protein 2570 peroxidase (emb|CAA66960.1) 2571 putative protein 2572 hypothetical protein 2573 glycine-rich protein 2 (GRP2) 2574 unknown protein 2575 berberine bridge enzyme-like protein 2576 unknown protein 2577 putative WD-repeat protein 2578 serine/threonine kinase-like protein 2579 serine/threonine kinase-like protein 2580 Cu2+-transporting ATPase-like protein 2581 translation initiation factor eIF4E 2582 O-methyltransferase-like protein 2583 translation initiation factor eIF3- like protein 2584 No function assigned by TIGR 2585 unknown protein 2586 hypothetical protein 2587 unknown protein 2588 unknown protein 2589 glycine-rich protein like 2590 putative disease resistance protein 2591 putative Na+/Ca2+ antiporter 2592 putative hydroxymethylglutaryl- CoA lyase 2593 putative phosphoribosylaminoimidazole carboxylase 2594 SAR DNA-binding protein-like 2595 response regulator, putative 2596 fibrillin precursor-like protein 2597 beta-ketoacyl-CoA synthase (FIDDLEHEAD) 2598 lectin like protein 2599 No function assigned by TIGR 2600 acidic endochitinase (dbj|BAA21861.1) 2601 unknown protein 2602 hypothetical protein 2603 predicted OR23 protein of unknown function 2604 putative protein 2605 hypothetical protein 2606 glycerol-3-phosphate dehydrogenase 2607 hypothetical protein 2608 tat-binding protein, putative 2609 putative protein 2610 putative trehalose-6- phosphate phosphatase 2611 hypothetical protein 2612 putative flavonol 3-O- glucosyltransferase 2613 60S ribosomal protein L30 2614 putative auxin-induced protein 2615 putative nonspecific lipid- transfer protein precursor 2616 AtRerlA 2617 putative aquaporin (tonoplast intrinsic protein gamma) 2618 hypothetical protein 2619 putative alanine acetyl transferase 2620 putative NADP-dependent glyceraldehyde-3-phosphate dehydrogenase 2621 putative DNA binding protein 2622 putative cystathionine gamma-synthase 2623 unknown protein 2624 malate oxidoreductase (malic enzyme) 2625 unknown protein 2626 cyclic nucleotide-gated cation channel 2627 glyoxalase II, putative 2628 putative trypsin inhibitor 2629 unknown protein 2630 unknown protein 2631 unknown protein 2632 nucleosome assembly protein I-like protein 2633 membrane channel like protein 2634 anthocyanin2, putative 2635 TWIN SISTER OF FT (TSF) 2636 putative myb-related transcription factor 2637 hypothetical protein 2638 putative RING zinc finger protein 2639 amino acid transport protein AAT1 2640 putative protein 2641 putative protein 2642 xanthine dehydrogenase 2643 xanthine dehydrogenase-like protein 2644 receptor protein kinase (IRK1), putative 2645 dehydrin-like protein 2646 unknown protein 2647 aldehyde dehydrogenase homolog, putative 2648 Ran binding protein (AtRanBPlb) 2649 putative squamosa-promoter binding protein 2650 putative protein 2651 kinesin like protein 2652 putative cellulose synthase 2653 calmodulin (cam2) 2654 fibrillarin-like protein 2655 putative transmembrane protein G5p 2656 putative peroxidase 2657 putative SNF1-related protein kinase 2658 glutathione S-transferase, putative 2659 unknown protein 2660 hypothetical protein 2661 putative protein 2662 phosphatidylinositol-4-phosphate 5-kinase isolog 2663 putative tyrosine decarboxylase 2664 unknown protein 2665 SGP1 monomeric G-protein (emb|CAB54517.1) 2666 putative serine carboxypeptidase II 2667 putative L5 ribosomal protein 2668 putative glucosyltransferase 2669 flavonoid 3,5-hydroxylase like protein 2670 putative protein 2671 putative protein 2672 putative Fe(II)/ascorbate oxidase 2673 putative anthocyanin 5- aromatic acyltransferase 2674 casein kinase I 2675 putative 2,3- bisphosphoglycerate- independent phosphoglycerate mutase 2676 putative glutathione S- transferase TSI-1 2677 ATP-dependent RNA helicase 2678 putative cytochrome P450 2679 putative WD-40 repeat protein 2680 No function assigned by TIGR 2681 No function assigned by TIGR 2682 putative protein 2683 putative extension 2684 nodulin-26-like protein 2685 RNA helicase (emb/CAA09212.1) 2686 predicted protein of unknown function 2687 putative berberine bridge enzyme 2688 thioredoxin, putative 2689 putative serine carboxypeptidase I 2690 cytochrome P450-like protein 2691 putative pyrophosphate-dependent phosphofructokinase alpha subunit 2692 putative flavonol glucosyltransferase 2693 peroxidase ATP20a (emb/CAA67338.1) 2694 TOPP8 serine/threonine protein phosphatase type one 2695 auxin regulated protein IAA18, putative 2696 putative WRKY-type DNA binding protein 2697 putative glucan synthase 2698 squalene monooxygenase 2699 putative proline-rich protein 2700 G2484-1 protein 2701 heat shock protein 70 like protein 2702 unknown protein 2703 unknown protein

TABLE 2 ABIOTIC STRESS RESPONSIVE GENE REGULATORY SEQUENCES SEQ REGULATORY ID NO: REGION 1 2704 2 2705 3 2706 4 2707 5 2708 6 2709 7 2710 8 2711 9 2712 10 2713 11 2714 12 2715 13 2716 14 2717 15 2718 16 2719 17 2720 18 2721 19 2722 20 2723 21 2724 22 2725 23 2726 24 2727 25 2728 26 2729 27 2730 28 2731 29 2732 30 2733 31 2734 32 2735 33 2736 34 2737 35 2738 36 2739 37 2740 38 2741 39 2742 40 2743 41 2744 42 2745 43 NONE 44 2746 45 2747 46 2748 47 2749 48 2750 49 2751 50 2752 51 2753 52 2754 53 2755 54 2756 55 2757 56 2758 57 2759 58 2760 59 2761 60 2762 61 2763 62 2764 63 2765 64 2766 65 2767 66 2768 67 2769 68 2770 69 NONE 70 2771 71 2772 72 2773 73 2774 74 2775 75 2776 76 2777 77 2778 78 2779 79 2780 80 2781 81 2782 82 2783 83 2784 84 2785 85 2786 86 2787 87 2788 88 2789 89 2790 90 2791 91 2792 92 2793 93 2794 94 2795 95 2796 96 2797 97 2798 98 2799 99 2800 100 2801 101 2802 102 2803 103 2804 104 2805 105 2806 106 2807 107 2808 108 2809 109 2810 110 2811 111 2812 112 2813 113 2814 114 2815 115 2816 116 2817 117 2818 118 2819 119 2820 120 2821 121 2822 122 2823 123 2824 124 2825 125 2826 126 2827 127 2828 128 2829 129 2830 130 2831 131 2832 132 2833 133 2834 134 2835 135 2836 136 2837 137 2838 138 2839 139 2840 140 2841 141 2842 142 2843 143 2844 144 NONE 145 2845 146 2846 147 2847 148 2848 149 2849 150 2850 151 2851 152 2852 153 2853 154 2854 155 2855 156 2856 157 2857 158 2858 159 2859 160 2860 161 2861 162 2862 163 2863 164 2864 165 2865 166 2866 167 2867 168 2868 169 2869 170 2870 171 2871 172 2872 173 2873 174 2874 175 2875 176 2876 177 2877 178 2878 179 2879 180 2880 181 2881 182 2882 183 2883 184 2884 185 2885 186 2886 187 2887 188 2888 189 2889 190 2890 191 2891 192 2892 193 2893 194 2894 195 2895 196 2896 197 2897 198 2898 199 2899 200 2900 201 2901 202 2902 203 2903 204 2904 205 2905 206 2906 207 2907 208 2908 209 2909 210 2910 211 2911 212 2912 213 2913 214 2914 215 2915 216 2916 217 2917 218 2918 219 2919 220 2920 221 2921 222 2922 223 2923 224 2924 225 2925 226 2926 227 2927 228 2928 229 2929 230 2930 231 2931 232 2932 233 2933 234 2934 235 2935 236 2936 237 2937 238 2938 239 2939 240 2940 241 2941 242 2942 243 2943 244 2944 245 2945 246 2946 247 2947 248 2948 249 2949 250 2950 251 2951 252 2952 253 2953 254 2954 255 2955 256 2956 257 2957 258 2958 259 2959 260 2960 261 2961 262 2962 263 2963 264 2964 265 2965 266 2966 267 2967 268 2968 269 2969 270 2970 271 2971 272 2972 273 2973 274 2974 275 2975 276 2976 277 2977 278 2978 279 2979 280 2980 281 2981 282 2982 283 2983 284 2984 285 2985 286 2986 287 2987 288 2988 289 2989 290 2990 291 2991 292 2992 293 2993 294 2994 295 2995 296 2996 297 2997 298 2998 299 2999 300 3000 301 3001 302 3002 303 3003 304 NONE 305 3004 306 3005 307 3006 308 3007 309 3008 310 3009 311 3010 312 3011 313 3012 314 3013 315 3014 316 3015 317 3016 318 3017 319 3018 320 3019 321 3020 322 3021 323 3022 324 3023 325 3024 326 3025 327 3026 328 3027 329 3028 330 3029 331 3030 332 3031 333 3032 334 3033 335 3034 336 3035 337 3036 338 3037 339 3038 340 3039 341 3040 342 3041 343 3042 344 3043 345 3044 346 3045 347 3046 348 3047 349 3048 350 3049 351 3050 352 3051 353 3052 354 3053 355 3054 356 3055 357 3056 358 3057 359 3058 360 3059 361 3060 362 3061 363 3062 364 3063 365 3064 366 3065 367 3066 368 3067 369 3068 370 3069 371 3070 372 3071 373 3072 374 3073 375 3074 376 3075 377 3076 378 3077 379 3078 380 3079 381 3080 382 3081 383 3082 384 3083 385 3084 386 3085 387 3086 388 3087 389 3088 390 3089 391 3090 392 3091 393 3092 394 3093 395 3094 396 3095 397 3096 398 3097 399 3098 400 3099 401 3100 402 3101 403 3102 404 3103 405 3104 406 3105 407 3106 408 3107 409 3108 410 3109 411 3110 412 3111 413 3112 414 3113 415 3114 416 3115 417 3116 418 3117 419 3118 420 3119 421 3120 422 3121 423 3122 424 3123 425 3124 426 3125 427 3126 428 3127 429 3128 430 3129 431 3130 432 3131 433 3132 434 3133 435 3134 436 3135 437 3136 438 3137 439 3138 440 3139 441 3140 442 3141 443 3142 444 3143 445 3144 446 3145 447 3146 448 3147 449 3148 450 3149 451 3150 452 3151 453 3152 454 3153 455 3154 456 3155 457 3156 458 3157 459 3158 460 3159 461 3160 462 3161 463 3162 464 3163 465 3164 466 3165 467 3166 468 3167 469 3168 470 3169 471 3170 472 3171 473 3172 474 3173 475 3174 476 3175 477 3176 478 3177 479 3178 480 3179 481 3180 482 3181 483 3182 484 3183 485 3184 486 3185 487 3186 488 3187 489 3188 490 3189 491 3190 492 3191 493 3192 494 3193 495 3194 496 3195 497 3196 498 3197 499 3198 500 3199 501 3200 502 3201 503 3202 504 3203 505 3204 506 3205 507 3206 508 3207 509 3208 510 3209 511 3210 512 3211 513 3212 514 3213 515 3214 516 3215 517 3216 518 3217 519 3218 520 3219 521 3220 522 3221 523 3222 524 3223 525 3224 526 3225 527 3226 528 3227 529 3228 530 3229 531 3230 532 3231 533 3232 534 3233 535 3234 536 3235 537 3236 538 3237 539 3238 540 3239 541 3240 542 3241 543 3242 544 3243 545 3244 546 3245 547 3246 548 3247 549 3248 550 3249 551 3250 552 3251 553 3252 554 3253 555 3254 556 3255 557 3256 558 3257 559 3258 560 3259 561 3260 562 3261 563 3262 564 3263 565 3264 566 3265 567 3266 568 3267 569 3268 570 3269 571 3270 572 3271 573 3272 574 3273 575 3274 576 3275 577 3276 578 3277 579 3278 580 3279 581 3280 582 3281 583 3282 584 3283 585 3284 586 3285 587 3286 588 3287 589 3288 590 3289 591 3290 592 3291 593 3292 594 3293 595 3294 596 3295 597 3296 598 3297 599 3298 600 3299 601 3300 602 3301 603 3302 604 3303 605 3304 606 3305 607 3306 608 3307 609 3308 610 3309 611 3310 612 3311 613 3312 614 3313 615 3314 616 3315 617 3316 618 3317 619 3318 620 3319 621 3320 622 3321 623 3322 624 3323 625 3324 626 3325 627 3326 628 3327 629 3328 630 3329 631 3330 632 3331 633 3332 634 3333 635 3334 636 3335 637 3336 638 3337 639 3338 640 3339 641 3340 642 3341 643 3342 644 3343 645 3344 646 3345 647 3346 648 3347 649 3348 650 3349 651 3350 652 3351 653 3352 654 3353 655 3354 656 3355 657 3356 658 3357 659 3358 660 3359 661 3360 662 3361 663 3362 664 3363 665 3364 666 3365 667 3366 668 3367 669 3368 670 3369 671 3370 672 3371 673 3372 674 3373 675 3374 676 3375 677 3376 678 3377 679 3378 680 3379 681 3380 682 3381 683 3382 684 3383 685 3384 686 3385 687 3386 688 3387 689 3388 690 3389 691 3390 692 3391 693 3392 694 3393 695 3394 696 3395 697 3396 698 3397 699 3398 700 3399 701 3400 702 3401 703 3402 704 3403 705 3404 706 3405 707 3406 708 3407 709 3408 710 3409 711 3410 712 3411 713 3412 714 3413 715 3414 716 3415 717 3416 718 3417 719 3418 720 3419 721 3420 722 3421 723 3422 724 3423 725 3424 726 3425 727 3426 728 3427 729 3428 730 3429 731 3430 732 3431 733 3432 734 3433 735 3434 736 3435 737 3436 738 3437 739 3438 740 3439 741 3440 742 3441 743 3442 744 3443 745 3444 746 3445 747 3446 748 3447 749 3448 750 3449 751 3450 752 3451 753 3452 754 3453 755 3454 756 3455 757 3456 758 3457 759 3458 760 3459 761 3460 762 3461 763 3462 764 3463 765 3464 766 3465 767 3466 768 3467 769 3468 770 3469 771 3470 772 3471 773 3472 774 3473 775 3474 776 3475 777 3476 778 3477 779 3478 780 3479 781 3480 782 3481 783 3482 784 3483 785 3484 786 3485 787 3486 788 3487 789 3488 790 3489 791 3490 792 3491 793 3492 794 3493 795 3494 796 3495 797 3496 798 3497 799 3498 800 3499 801 3500 802 3501 803 3502 804 3503 805 3504 806 3505 807 3506 808 3507 809 3508 810 3509 811 3510 812 3511 813 3512 814 3513 815 3514 816 3515 817 3516 818 3517 819 3518 820 3519 821 3520 822 3521 823 3522 824 3523 825 3524 826 3525 827 3526 828 3527 829 3528 830 3529 831 3530 832 3531 833 3532 834 3533 835 3534 836 3535 837 3536 838 3537 839 3538 840 3539 841 3540 842 3541 843 3542 844 3543 845 3544 846 3545 847 3546 848 3547 849 3548 850 3549 851 3550 852 3551 853 3552 854 3553 855 3554 856 3555 857 3556 858 3557 859 3558 860 3559 861 3560 862 3561 863 3562 864 3563 865 3564 866 3565 867 3566 868 3567 869 3568 870 3569 871 3570 872 3571 873 3572 874 3573 875 3574 876 3575 877 3576 878 3577 879 3578 880 3579 881 3580 882 3581 883 3582 884 3583 885 3584 886 3585 887 NONE 888 3586 889 3587 890 3588 891 3589 892 3590 893 3591 894 NONE 895 NONE 896 3592 897 3593 898 3594 899 3595 900 3596 901 3597 902 3598 903 3599 904 3600 905 3601 906 3602 907 3603 908 3604 909 3605 910 3606 911 3607 912 3608 913 3609 914 3610 915 3611 916 3612 917 3613 918 3614 919 3615 920 3616 921 3617 922 3618 923 3619 924 3620 925 3621 926 3622 927 3623 928 3624 929 3625 930 3626 931 3627 932 3628 933 3629 934 3630 935 NONE 936 3631 937 3632 938 3633 939 3634 940 3635 941 3636 942 3637 943 3638 944 3639 945 3640 946 3641 947 3642 948 3643 949 3644 950 3645 951 3646 952 3647 953 3648 954 3649 955 3650 956 3651 957 3652 958 3653 959 3654 960 3655 961 3656 962 3657 963 3658 964 3659 965 3660 966 3661 967 3662 968 3663 969 3664 970 3665 971 3666 972 3667 973 3668 974 3669 975 3670 976 3671 977 3672 978 3673 979 3674 980 3675 981 3676 982 3677 983 3678 984 3679 985 3680 986 3681 987 3682 988 3683 989 3684 990 3685 991 3686 992 3687 993 3688 994 3689 995 3690 996 3691 997 3692 998 3693 999 3694 1000 3695 1001 3696 1002 3697 1003 3698 1004 3699 1005 3700 1006 3701 1007 3702 1008 3703 1009 3704 1010 3705 1011 3706 1012 3707 1013 3708 1014 3709 1015 3710 1016 3711 1017 3712 1018 3713 1019 3714 1020 3715 1021 3716 1022 3717 1023 3718 1024 3719 1025 3720 1026 3721 1027 3722 1028 3723 1029 3724 1030 3725 1031 3726 1032 3727 1033 3728 1034 3729 1035 3730 1036 3731 1037 3732 1038 3733 1039 3734 1040 3735 1041 3736 1042 3737 1043 3738 1044 3739 1045 3740 1046 3741 1047 3742 1048 3743 1049 3744 1050 3745 1051 3746 1052 3747 1053 3748 1054 3749 1055 3750 1056 3751 1057 3752 1058 3753 1059 3754 1060 3755 1061 3756 1062 3757 1063 3758 1064 3759 1065 3760 1066 3761 1067 3762 1068 3763 1069 3764 1070 3765 1071 3766 1072 3767 1073 3768 1074 3769 1075 3770 1076 3771 1077 3772 1078 3773 1079 3774 1080 3775 1081 3776 1082 3777 1083 3778 1084 3779 1085 3780 1086 3781 1087 NONE 1088 3782 1089 3783 1090 3784 1091 3785 1092 3786 1093 3787 1094 3788 1095 3789 1096 3790 1097 3791 1098 3792 1099 3793 1100 3794 1101 3795 1102 3796 1103 3797 1104 3798 1105 3799 1106 3800 1107 3801 1108 3802 1109 3803 1110 3804 1111 3805 1112 3806 1113 3807 1114 3808 1115 3809 1116 3810 1117 3811 1118 3812 1119 3813 1120 3814 1121 3815 1122 3816 1123 3817 1124 3818 1125 3819 1126 3820 1127 3821 1128 3822 1129 3823 1130 3824 1131 3825 1132 3826 1133 3827 1134 3828 1135 3829 1136 3830 1137 3831 1138 3832 1139 3833 1140 3834 1141 3835 1142 3836 1143 3837 1144 3838 1145 3839 1146 3840 1147 3841 1148 3842 1149 3843 1150 3844 1151 3845 1152 3846 1153 3847 1154 3848 1155 3849 1156 3850 1157 3851 1158 3852 1159 3853 1160 3854 1161 3855 1162 3856 1163 3857 1164 3858 1165 3859 1166 3860 1167 3861 1168 3862 1169 3863 1170 3864 1171 3865 1172 3866 1173 3867 1174 3868 1175 3869 1176 3870 1177 3871 1178 3872 1179 3873 1180 3874 1181 3875 1182 3876 1183 3877 1184 3878 1185 3879 1186 3880 1187 3881 1188 3882 1189 3883 1190 3884 1191 3885 1192 3886 1193 3887 1194 3888 1195 3889 1196 3890 1197 3891 1198 3892 1199 3893 1200 3894 1201 3895 1202 3896 1203 3897 1204 3898 1205 3899 1206 3900 1207 3901 1208 3902 1209 3903 1210 3904 1211 3905 1212 3906 1213 3907 1214 3908 1215 3909 1216 3910 1217 3911 1218 3912 1219 3913 1220 3914 1221 3915 1222 3916 1223 3917 1224 3918 1225 3919 1226 3920 1227 3921 1228 3922 1229 3923 1230 3924 1231 3925 1232 3926 1233 3927 1234 3928 1235 3929 1236 3930 1237 3931 1238 3932 1239 3933 1240 3934 1241 3935 1242 3936 1243 3937 1244 3938 1245 3939 1246 3940 1247 3941 1248 3942 1249 3943 1250 3944 1251 3945 1252 3946 1253 3947 1254 3948 1255 3949 1256 3950 1257 3951 1258 3952 1259 3953 1260 3954 1261 3955 1262 3956 1263 3957 1264 3958 1265 3959 1266 3960 1267 3961 1268 3962 1269 3963 1270 3964 1271 3965 1272 3966 1273 3967 1274 3968 1275 3969 1276 3970 1277 3971 1278 3972 1279 3973 1280 3974 1281 3975 1282 3976 1283 3977 1284 3978 1285 3979 1286 3980 1287 3981 1288 3982 1289 3983 1290 3984 1291 3985 1292 3986 1293 3987 1294 3988 1295 3989 1296 3990 1297 3991 1298 3992 1299 3993 1300 3994 1301 3995 1302 3996 1303 3997 1304 3998 1305 3999 1306 4000 1307 4001 1308 4002 1309 4003 1310 4004 1311 4005 1312 4006 1313 4007 1314 4008 1315 4009 1316 4010 1317 4011 1318 4012 1319 4013 1320 4014 1321 4015 1322 4016 1323 4017 1324 4018 1325 4019 1326 4020 1327 4021 1328 4022 1329 4023 1330 NONE 1331 4024 1332 4025 1333 4026 1334 4027 1335 4028 1336 4029 1337 4030 1338 4031 1339 4032 1340 4033 1341 4034 1342 4035 1343 4036 1344 4037 1345 4038 1346 4039 1347 4040 1348 4041 1349 4042 1350 4043 1351 4044 1352 4045 1353 4046 1354 4047 1355 4048 1356 4049 1357 4050 1358 4051 1359 4052 1360 4053 1361 4054 1362 4055 1363 4056 1364 4057 1365 4058 1366 4059 1367 4060 1368 4061 1369 4062 1370 4063 1371 4064 1372 4065 1373 4066 1374 4067 1375 4068 1376 4069 1377 4070 1378 4071 1379 4072 1380 4073 1381 4074 1382 4075 1383 4076 1384 4077 1385 4078 1386 4079 1387 4080 1388 4081 1389 4082 1390 4083 1391 4084 1392 4085 1393 4086 1394 4087 1395 4088 1396 4089 1397 4090 1398 4091 1399 4092 1400 4093 1401 4094 1402 4095 1403 4096 1404 4097 1405 4098 1406 4099 1407 4100 1408 4101 1409 4102 1410 4103 1411 4104 1412 4105 1413 4106 1414 4107 1415 4108 1416 4109 1417 4110 1418 4111 1419 4112 1420 4113 1421 4114 1422 4115 1423 4116 1424 4117 1425 4118 1426 4119 1427 4120 1428 4121 1429 4122 1430 4123 1431 4124 1432 NONE 1433 4125 1434 4126 1435 4127 1436 4128 1437 4129 1438 4130 1439 4131 1440 4132 1441 4133 1442 4134 1443 4135 1444 4136 1445 4137 1446 4138 1447 4139 1448 4140 1449 4141 1450 4142 1451 4143 1452 4144 1453 4145 1454 4146 1455 4147 1456 4148 1457 4149 1458 4150 1459 4151 1460 4152 1461 4153 1462 4154 1463 4155 1464 4156 1465 4157 1466 4158 1467 4159 1468 4160 1469 4161 1470 4162 1471 4163 1472 4164 1473 4165 1474 4166 1475 4167 1476 4168 1477 4169 1478 4170 1479 4171 1480 4172 1481 4173 1482 4174 1483 4175 1484 4176 1485 4177 1486 4178 1487 4179 1488 4180 1489 4181 1490 4182 1491 4183 1492 4184 1493 4185 1494 4186 1495 4187 1496 4188 1497 4189 1498 4190 1499 4191 1500 4192 1501 4193 1502 4194 1503 4195 1504 4196 1505 4197 1506 4198 1507 4199 1508 4200 1509 4201 1510 4202 1511 4203 1512 4204 1513 4205 1514 4206 1515 4207 1516 4208 1517 4209 1518 4210 1519 4211 1520 4212 1521 4213 1522 4214 1523 4215 1524 4216 1525 4217 1526 4218 1527 4219 1528 4220 1529 4221 1530 4222 1531 4223 1532 4224 1533 4225 1534 4226 1535 4227 1536 4228 1537 4229 1538 4230 1539 4231 1540 4232 1541 4233 1542 4234 1543 4235 1544 4236 1545 4237 1546 4238 1547 4239 1548 4240 1549 4241 1550 4242 1551 4243 1552 4244 1553 4245 1554 4246 1555 4247 1556 4248 1557 4249 1558 NONE 1559 4250 1560 4251 1561 4252 1562 4253 1563 4254 1564 4255 1565 4256 1566 4257 1567 4258 1568 4259 1569 4260 1570 4261 1571 4262 1572 4263 1573 4264 1574 4265 1575 4266 1576 4267 1577 4268 1578 4269 1579 4270 1580 4271 1581 4272 1582 4273 1583 4274 1584 4275 1585 4276 1586 4277 1587 4278 1588 4279 1589 4280 1590 4281 1591 4282 1592 4283 1593 4284 1594 4285 1595 4286 1596 4287 1597 4288 1598 4289 1599 4290 1600 4291 1601 4292 1602 4293 1603 4294 1604 4295 1605 4296 1606 4297 1607 4298 1608 4299 1609 4300 1610 4301 1611 4302 1612 4303 1613 4304 1614 4305 1615 4306 1616 4307 1617 4308 1618 4309 1619 4310 1620 4311 1621 4312 1622 4313 1623 4314 1624 4315 1625 4316 1626 4317 1627 4318 1628 4319 1629 4320 1630 4321 1631 4322 1632 4323 1633 4324 1634 4325 1635 4326 1636 4327 1637 4328 1638 4329 1639 4330 1640 4331 1641 4332 1642 4333 1643 4334 1644 4335 1645 4336 1646 4337 1647 4338 1648 4339 1649 4340 1650 4341 1651 4342 1652 4343 1653 4344 1654 4345 1655 4346 1656 4347 1657 4348 1658 4349 1659 4350 1660 4351 1661 4352 1662 4353 1663 NONE 1664 4354 1665 4355 1666 4356 1667 4357 1668 4358 1669 4359 1670 4360 1671 4361 1672 4362 1673 4363 1674 4364 1675 4365 1676 4366 1677 4367 1678 4368 1679 4369 1680 4370 1681 4371 1682 4372 1683 4373 1684 4374 1685 4375 1686 4376 1687 4377 1688 4378 1689 4379 1690 4380 1691 4381 1692 4382 1693 4383 1694 4384 1695 4385 1696 4386 1697 4387 1698 4388 1699 4389 1700 4390 1701 4391 1702 4392 1703 4393 1704 4394 1705 4395 1706 4396 1707 4397 1708 4398 1709 4399 1710 4400 1711 4401 1712 NONE 1713 4402 1714 4403 1715 4404 1716 4405 1717 4406 1718 4407 1719 4408 1720 4409 1721 4410 1722 4411 1723 4412 1724 4413 1725 4414 1726 4415 1727 4416 1728 4417 1729 4418 1730 4419 1731 4420 1732 4421 1733 4422 1734 4423 1735 4424 1736 4425 1737 4426 1738 4427 1739 4428 1740 4429 1741 4430 1742 4431 1743 4432 1744 4433 1745 4434 1746 4435 1747 4436 1748 4437 1749 4438 1750 4439 1751 4440 1752 4441 1753 4442 1754 4443 1755 4444 1756 4445 1757 4446 1758 4447 1759 4448 1760 4449 1761 4450 1762 4451 1763 4452 1764 4453 1765 4454 1766 4455 1767 4456 1768 4457 1769 4458 1770 4459 1771 4460 1772 4461 1773 4462 1774 4463 1775 4464 1776 4465 1777 4466 1778 4467 1779 4468 1780 4469 1781 4470 1782 4471 1783 4472 1784 NONE 1785 4473 1786 4474 1787 4475 1788 4476 1789 4477 1790 4478 1791 4479 1792 4480 1793 4481 1794 4482 1795 4483 1796 4484 1797 4485 1798 4486 1799 4487 1800 4488 1801 4489 1802 4490 1803 NONE 1804 4491 1805 4492 1806 4493 1807 4494 1808 4495 1809 4496 1810 4497 1811 4498 1812 4499 1813 4500 1814 4501 1815 4502 1816 4503 1817 4504 1818 4505 1819 4506 1820 4507 1821 4508 1822 4509 1823 4510 1824 4511 1825 4512 1826 4513 1827 4514 1828 4515 1829 4516 1830 4517 1831 4518 1832 4519 1833 4520 1834 4521 1835 4522 1836 4523 1837 4524 1838 4525 1839 4526 1840 4527 1841 4528 1842 4529 1843 4530 1844 4531 1845 4532 1846 4533 1847 4534 1848 4535 1849 4536 1850 4537 1851 4538 1852 4539 1853 4540 1854 4541 1855 4542 1856 4543 1857 4544 1858 4545 1859 4546 1860 4547 1861 4548 1862 4549 1863 4550 1864 4551 1865 4552 1866 4553 1867 4554 1868 4555 1869 4556 1870 4557 1871 4558 1872 4559 1873 4560 1874 4561 1875 4562 1876 4563 1877 4564 1878 4565 1879 4566 1880 4567 1881 4568 1882 4569 1883 4570 1884 4571 1885 4572 1886 4573 1887 4574 1888 4575 1889 4576 1890 4577 1891 4578 1892 4579 1893 4580 1894 4581 1895 4582 1896 4583 1897 NONE 1898 4584 1899 4585 1900 4586 1901 4587 1902 4588 1903 4589 1904 4590 1905 4591 1906 4592 1907 NONE 1908 4593 1909 4594 1910 4595 1911 4596 1912 4597 1913 4598 1914 4599 1915 4600 1916 4601 1917 4602 1918 4603 1919 4604 1920 4605 1921 4606 1922 4607 1923 4608 1924 4609 1925 4610 1926 4611 1927 4612 1928 4613 1929 4614 1930 4615 1931 4616 1932 4617 1933 4618 1934 4619 1935 4620 1936 4621 1937 4622 1938 4623 1939 4624 1940 4625 1941 4626 1942 4627 1943 4628 1944 4629 1945 4630 1946 4631 1947 4632 1948 4633 1949 4634 1950 4635 1951 4636 1952 4637 1953 4638 1954 4639 1955 4640 1956 4641 1957 4642 1958 4643 1959 4644 1960 4645 1961 4646 1962 4647 1963 4648 1964 4649 1965 4650 1966 4651 1967 4652 1968 4653 1969 4654 1970 4655 1971 4656 1972 4657 1973 4658 1974 4659 1975 4660 1976 4661 1977 4662 1978 4663 1979 4664 1980 4665 1981 4666 1982 4667 1983 4668 1984 4669 1985 4670 1986 4671 1987 4672 1988 4673 1989 4674 1990 4675 1991 4676 1992 4677 1993 4678 1994 4679 1995 4680 1996 4681 1997 4682 1998 4683 1999 4684 2000 4685 2001 4686 2002 4687 2003 4688 2004 4689 2005 4690 2006 4691 2007 4692 2008 4693 2009 4694 2010 4695 2011 4696 2012 4697 2013 4698 2014 4699 2015 4700 2016 4701 2017 4702 2018 4703 2019 4704 2020 4705 2021 4706 2022 4707 2023 4708 2024 4709 2025 4710 2026 4711 2027 4712 2028 4713 2029 4714 2030 NONE 2031 4715 2032 4716 2033 4717 2034 4718 2035 4719 2036 4720 2037 4721 2038 4722 2039 4723 2040 4724 2041 4725 2042 4726 2043 4727 2044 4728 2045 4729 2046 4730 2047 4731 2048 4732 2049 4733 2050 4734 2051 4735 2052 4736 2053 4737 2054 4738 2055 4739 2056 4740 2057 4741 2058 4742 2059 4743 2060 4744 2061 4745 2062 4746 2063 4747 2064 4748 2065 4749 2066 4750 2067 4751 2068 4752 2069 4753 2070 4754 2071 4755 2072 4756 2073 4757 2074 4758 2075 4759 2076 4760 2077 4761 2078 4762 2079 4763 2080 4764 2081 4765 2082 4766 2083 4767 2084 4768 2085 4769 2086 4770 2087 4771 2088 4772 2089 4773 2090 4774 2091 4775 2092 4776 2093 4777 2094 4778 2095 4779 2096 4780 2097 4781 2098 4782 2099 4783 2100 4784 2101 4785 2102 4786 2103 4787 2104 4788 2105 4789 2106 4790 2107 4791 2108 4792 2109 4793 2110 4794 2111 4795 2112 4796 2113 4797 2114 4798 2115 4799 2116 4800 2117 4801 2118 4802 2119 4803 2120 4804 2121 4805 2122 4806 2123 4807 2124 4808 2125 4809 2126 4810 2127 4811 2128 4812 2129 4813 2130 4814 2131 4815 2132 4816 2133 4817 2134 4818 2135 4819 2136 4820 2137 4821 2138 4822 2139 4823 2140 4824 2141 4825 2142 4826 2143 4827 2144 4828 2145 4829 2146 4830 2147 4831 2148 4832 2149 4833 2150 4834 2151 NONE 2152 4835 2153 4836 2154 4837 2155 4838 2156 4839 2157 4840 2158 4841 2159 4842 2160 4843 2161 4844 2162 4845 2163 4846 2164 4847 2165 4848 2166 4849 2167 4850 2168 4851 2169 4852 2170 4853 2171 4854 2172 4855 2173 4856 2174 4857 2175 4858 2176 4859 2177 4860 2178 4861 2179 4862 2180 4863 2181 4864 2182 4865 2183 4866 2184 4867 2185 4868 2186 4869 2187 4870 2188 4871 2189 4872 2190 4873 2191 4874 2192 4875 2193 4876 2194 4877 2195 4878 2196 4879 2197 4880 2198 4881 2199 4882 2200 4883 2201 4884 2202 4885 2203 4886 2204 4887 2205 4888 2206 4889 2207 4890 2208 4891 2209 4892 2210 4893 2211 4894 2212 4895 2213 4896 2214 4897 2215 4898 2216 4899 2217 4900 2218 4901 2219 4902 2220 4903 2221 4904 2222 4905 2223 4906 2224 4907 2225 4908 2226 4909 2227 4910 2228 4911 2229 4912 2230 4913 2231 4914 2232 4915 2233 4916 2234 4917 2235 4918 2236 4919 2237 4920 2238 4921 2239 4922 2240 4923 2241 4924 2242 4925 2243 4926 2244 4927 2245 4928 2246 4929 2247 4930 2248 NONE 2249 4931 2250 4932 2251 4933 2252 4934 2253 4935 2254 4936 2255 4937 2256 4938 2257 4939 2258 4940 2259 4941 2260 4942 2261 4943 2262 4944 2263 4945 2264 4946 2265 4947 2266 4948 2267 4949 2268 4950 2269 4951 2270 4952 2271 4953 2272 4954 2273 4955 2274 4956 2275 4957 2276 4958 2277 4959 2278 4960 2279 4961 2280 4962 2281 4963 2282 4964 2283 4965 2284 4966 2285 4967 2286 4968 2287 4969 2288 4970 2289 4971 2290 4972 2291 4973 2292 4974 2293 4975 2294 4976 2295 4977 2296 4978 2297 4979 2298 4980 2299 4981 2300 4982 2301 4983 2302 4984 2303 4985 2304 4986 2305 4987 2306 4988 2307 4989 2308 4990 2309 4991 2310 4992 2311 4993 2312 4994 2313 4995 2314 4996 2315 4997 2316 4998 2317 4999 2318 5000 2319 5001 2320 5002 2321 5003 2322 5004 2323 5005 2324 5006 2325 5007 2326 5008 2327 5009 2328 5010 2329 5011 2330 5012 2331 5013 2332 5014 2333 5015 2334 5016 2335 5017 2336 5018 2337 5019 2338 5020 2339 5021 2340 NONE 2341 5022 2342 5023 2343 5024 2344 5025 2345 5026 2346 5027 2347 5028 2348 5029 2349 5030 2350 5031 2351 5032 2352 5033 2353 5034 2354 5035 2355 5036 2356 5037 2357 5038 2358 5039 2359 5040 2360 5041 2361 5042 2362 5043 2363 5044 2364 5045 2365 5046 2366 5047 2367 5048 2368 5049 2369 5050 2370 5051 2371 NONE 2372 5052 2373 5053 2374 5054 2375 5055 2376 5056 2377 5057 2378 5058 2379 5059 2380 5060 2381 5061 2382 5062 2383 5063 2384 5064 2385 5065 2386 5066 2387 5067 2388 5068 2389 5069 2390 5070 2391 5071 2392 5072 2393 5073 2394 5074 2395 5075 2396 5076 2397 5077 2398 5078 2399 5079 2400 5080 2401 5081 2402 5082 2403 5083 2404 5084 2405 5085 2406 5086 2407 5087 2408 5088 2409 5089 2410 5090 2411 5091 2412 5092 2413 5093 2414 5094 2415 5095 2416 5096 2417 5097 2418 5098 2419 5099 2420 5100 2421 5101 2422 5102 2423 5103 2424 5104 2425 5105 2426 5106 2427 5107 2428 5108 2429 5109 2430 5110 2431 5111 2432 5112 2433 5113 2434 5114 2435 5115 2436 5116 2437 5117 2438 5118 2439 5119 2440 5120 2441 5121 2442 5122 2443 NONE 2444 5123 2445 5124 2446 5125 2447 5126 2448 5127 2449 5128 2450 5129 2451 5130 2452 5131 2453 5132 2454 5133 2455 5134 2456 5135 2457 5136 2458 5137 2459 5138 2460 5139 2461 5140 2462 5141 2463 5142 2464 5143 2465 5144 2466 5145 2467 5146 2468 5147 2469 NONE 2470 5148 2471 5149 2472 5150 2473 5151 2474 5152 2475 5153 2476 5154 2477 5155 2478 5156 2479 5157 2480 5158 2481 5159 2482 5160 2483 5161 2484 5162 2485 5163 2486 5164 2487 5165 2488 5166 2489 5167 2490 5168 2491 5169 2492 5170 2493 5171 2494 5172 2495 5173 2496 5174 2497 5175 2498 5176 2499 5177 2500 5178 2501 5179 2502 5180 2503 5181 2504 5182 2505 5183 2506 5184 2507 5185 2508 5186 2509 5187 2510 5188 2511 5189 2512 5190 2513 5191 2514 5192 2515 5193 2516 5194 2517 5195 2518 5196 2519 5197 2520 5198 2521 5199 2522 5200 2523 5201 2524 5202 2525 5203 2526 5204 2527 5205 2528 5206 2529 5207 2530 5208 2531 5209 2532 5210 2533 5211 2534 5212 2535 5213 2536 5214 2537 5215 2538 5216 2539 5217 2540 5218 2541 5219 2542 5220 2543 5221 2544 5222 2545 5223 2546 5224 2547 5225 2548 5226 2549 5227 2550 5228 2551 5229 2552 5230 2553 5231 2554 5232 2555 5233 2556 5234 2557 5235 2558 5236 2559 5237 2560 5238 2561 5239 2562 5240 2563 5241 2564 5242 2565 5243 2566 5244 2567 5245 2568 5246 2569 5247 2570 5248 2571 5249 2572 5250 2573 5251 2574 5252 2575 5253 2576 5254 2577 5255 2578 5256 2579 5257 2580 5258 2581 5259 2582 5260 2583 5261 2584 5262 2585 5263 2586 5264 2587 5265 2588 5266 2589 5267 2590 5268 2591 5269 2592 5270 2593 5271 2594 5272 2595 5273 2596 5274 2597 5275 2598 5276 2599 NONE 2600 5277 2601 5278 2602 5279 2603 5280 2604 5281 2605 5282 2606 5283 2607 5284 2608 5285 2609 5286 2610 5287 2611 5288 2612 5289 2613 5290 2614 5291 2615 5292 2616 5293 2617 5294 2618 5295 2619 5296 2620 5297 2621 5298 2622 5299 2623 5300 2624 5301 2625 5302 2626 5303 2627 5304 2628 5305 2629 5306 2630 5307 2631 5308 2632 5309 2633 5310 2634 5311 2635 5312 2636 5313 2637 5314 2638 5315 2639 5316 2640 5317 2641 5318 2642 5319 2643 5320 2644 5321 2645 5322 2646 5323 2647 5324 2648 5325 2649 5326 2650 5327 2651 5328 2652 5329 2653 5330 2654 5331 2655 5332 2656 5333 2657 5334 2658 5335 2659 5336 2660 5337 2661 5338 2662 5339 2663 5340 2664 5341 2665 5342 2666 5343 2667 5344 2668 5345 2669 5346 2670 5347 2671 5348 2672 5349 2673 5350 2674 5351 2675 5352 2676 5353 2677 5354 2678 5355 2679 5356 2680 5357 2681 NONE 2682 5358 2683 5359 2684 5360 2685 5361 2686 5362 2687 5363 2688 5364 2689 5365 2690 5366 2691 5367 2692 5368 2693 5369 2694 5370 2695 5371 2696 5372 2697 5373 2698 5374 2699 5375 2700 5376 2701 5377 2702 5378 2703 5379

TABLE 3 COLD RESPONSIVE SEQUENCES SEQ AFFYMETRIX ID NO: ID NO: 1 11991_G_AT 2 11992_AT 3 11997_AT 4 11998_AT 5 12001_AT 6 12006_S_AT 7 12007_AT 8 12009_AT 9 12018_AT 10 12022_AT 11 12026_AT 12 12031_AT 13 12047_AT 14 12051_AT 15 12052_AT 16 12053_AT 17 12060_AT 18 12072_AT 19 12074_AT 20 12102_AT 21 12112_AT 22 12117_AT 23 12125_AT 24 12130_AT 25 12143_AT 26 12145_S_AT 27 12149_AT 28 12156_AT 29 12163_AT 30 12166_I_AT 31 12167_AT 32 12169_I_AT 33 12175_AT 34 12176_AT 35 12179_AT 36 12187_AT 15920_I_AT 37 12195_AT 38 12196_AT 39 12198_AT 40 12200_AT 41 12202_AT 42 12214_G_AT 43 12219_AT 44 12224_AT 45 12226_AT 46 12233_AT 47 12240_AT 48 12253_G_AT 49 12256_AT 50 12269_S_AT 51 12270_AT 52 12284_AT 53 12287_S_AT 17570_G_AT 54 12293_AT 55 12294_S_AT 56 12300_AT 57 12307_AT 58 12312_AT 59 12315_AT 60 12324_I_AT 61 12331_S_AT 62 12336_AT 63 12344_AT 64 12348_AT 65 12353_AT 66 12359_S_AT 67 12372_AT 68 12374_I_AT 12726_F_AT 69 12390_AT 70 12395_S_AT 71 12405_AT 72 12408_AT 73 12410_G_AT 74 12419_AT 75 12427_AT 76 12431_AT 77 12436_AT 78 12438_AT 79 12443_S_AT 80 12447_AT 81 12450_S_AT 82 12452_AT 83 12474_AT 84 12477_AT 85 12491_AT 86 12497_AT 87 12500_S_AT 88 12503_AT 89 12515_AT 90 12516_S_AT 91 12523_AT 92 12526_AT 93 12527_AT 94 12532_AT 95 12534_G_AT 96 12544_AT 97 12549_S_AT 98 12550_S_AT 17103_S_AT 99 12552_AT 100 12555_S_AT 101 12576_S_AT 102 12581_S_AT 16645_S_AT 103 12587_AT 104 12597_AT 105 12602_AT 106 12610_AT 107 12631_AT 108 12646_AT 109 12649_AT 110 12650_AT 111 12653_AT 112 12661_AT 113 12666_AT 114 12674_AT 115 12675_S_AT 116 12678_I_AT 117 12681_S_AT 118 12688_AT 119 12702_AT 120 12705_F_AT 121 12736_F_AT 122 12737_F_AT 123 12758_AT 124 12760_G_AT 125 12762_R_AT 126 12764_F_AT 127 12766_AT 15115_F_AT 128 12767_AT 129 12768_AT 130 12772_AT 131 12773_AT 132 12776_AT 133 12788_AT 134 12793_AT 135 12794_AT 136 12802_AT 137 12809_G_AT 138 12812_AT 139 12815_AT 140 12816_AT 141 12818_AT 142 12824_S_AT 143 12828_S_AT 144 12842_S_AT

TABLE 4 2X UP IN COLD, ONLY 11997_at 11998_at 12018_at 12031_at 12047_at 12051_at 12053_at 12060_at 12072_at 12074_at 12102_at 12112_at 12117_at 12130_at 12145_s_at 12151_at 12163_at 12175_at 12187_at 12195_at 12219_at 12256_at 12269_s_at 12307_at 12315_at 12336_at 12349_s_at 12353_at 12359_s_at 12390_at 12395_s_at 12431_at 12436_at 12443_s_at 12447_at 12452_at 12477_at 12503_at 12516_s_at 12532_at 12544_at 12561_at 12602_at 12610_at 12631_at 12647_s_at 12650_at 12656_at 12674_at 12675_s_at 12676_s_at 12681_s_at 12686_s_at 12688_at 12701_i_at 12702_at 12719_f_at 12726_f_at 12736_f_at 12754_g_at 12762_r_at 12766_at 12767_at 12768_at 12773_at 12788_at 12802_at 12860_s_at 12861_s_at 12879_s_at 12891_at 12914_s_at 12927_s_at 12947_at 12956_i_at 12966_s_at 12974_at 12987_s_at 12994_s_at 12998_at 13002_at 13018_at 13023_at 13046_g_at 13054_at 13086_r_at 13087_at 13100_at 13109_at 13119_at 13120_at 13128_at 13134_s_at 13140_at 13143_at 13167_at 13172_s_at 13178_at 13179_at 13181_at 13187_i_at 13209_s_at 13219_s_at 13221_at 13243_r_at 13260_s_at 13274_s_at 13278_f_at 13279_s_at 13285_s_at 13288_s_at 13292_s_at 13297_s_at 13299_s_at 13332_at 13351_at 13352_at 13422_at 13435_at 13461_s_at 13467_at 13488_at 13495_s_at 13539_i_at 13542_at 13575_at 13577_s_at 13617_at 13634_s_at 13656_at 13671_s_at 13691_s_at 13700_at 13704_s_at 13709_s_at 13715_at 13785_at 13803_at 13812_s_at 13825_s_at 13850_i_at 13904_s_at 13908_s_at 13927_at 13971_s_at 13985_s_at 14013_at 14019_at 14021_r_at 14028_at 14048_at 14058_at 14059_at 14064_at 14073_at 14105_at 14106_at 14126_s_at 14140_at 14145_at 14170_at 14186_at 14196_at 14227_at 14234_at 14250_r_at 14270_at 14298_g_at 14303_s_at 14312_at 14339_at 14388_at 14393_at 14511_at 14525_s_at 14527_at 14534_s_at 14554_at 14566_at 14579_at 14591_at 14595_at 14600_at 14631_s_at 14635_s_at 14679_s_at 14691_at 14697_g_at 14709_at 14711_s_at 14728_s_at 14731_s_at 14797_s_at 14809_at 14843_at 14847_at 14872_at 14886_at 14896_at 14897_at 14900_at 14956_s_at 14958_at 14965_at 14984_s_at 15004_at 15010_at 15036_r_at 15040_g_at 15046_s_at 15057_at 15073_at 15083_at 15084_at 15096_at 15101_s_at 15105_s_at 15112_s_at 15115_f_at 15116_f_at 15122_s_at 15126_s_at 15131_s_at 15132_s_at 15137_s_at 15144_s_at 15148_s_at 15153_s_at 15159_s_at 15160_s_at 15166_s_at 15174_f_at 15197_s_at 15270_at 15319_at 15325_at 15337_at 15341_at 15343_at 15355_s_at 15367_at 15379_at 15381_at 15410_at 15417_s_at 15422_at 15433_at 15451_at 15452_at 15453_s_at 15472_at 15489_at 15490_at 15503_at 15510_r_at 15517_s_at 15518_at 15544_at 15588_s_at 15600_s_at 15605_s_at 15613_s_at 15614_s_at 15616_s_at 15633_s_at 15639_s_at 15641_s_at 15660_s_at 15665_s_at 15687_f_at 15694_s_at 15712_s_at 15783_s_at 15808_at 15837_at 15850_at 15862_at 15868_at 15878_at 15901_at 15912_at 15920_i_at 15941_at 15945_at 15960_at 15990_at 16001_at 16009_s_at 16010_s_at 16034_at 16036_i_at 16039_s_at 16040_at 16042_s_at 16047_at 16049_s_at 16051_s_at 16062_s_at 16079_s_at 16087_s_at 16090_s_at 16117_s_at 16118_s_at 16137_s_at 16155_s_at 16162_s_at 16184_at 16192_at 16222_at 16244_at 16250_at 16260_at 16286_at 16296_at 16297_at 16342_at 16367_i_at 16411_s_at 16442_s_at 16465_at 16466_s_at 16468_at 16486_at 16487_at 16488_at 16489_at 16496_s_at 16499_at 16511_at 16517_at 16538_s_at 16554_s_at 16571_s_at 16576_f_at 16595_s_at 16605_s_at 16610_s_at 16620_s_at 16621_s_at 16635_s_at 16636_s_at 16638_s_at 16650_s_at 16672_at 16673_at 16687_s_at 16747_at 16753_at 16768_at 16805_s_at 16807_at 16845_at 16847_at 16896_s_at 16899_at 16902_at 16911_at 16914_s_at 16943_s_at 16956_at 16996_s_at 17010_s_at 17016_s_at 17032_s_at 17033_s_at 17043_s_at 17050_s_at 17055_s_at 17068_s_at 17071_s_at 17075_s_at 17077_s_at 17102_s_at 17109_s_at 17113_s_at 17123_s_at 17128_s_at 17129_s_at 17132_at 17166_at 17206_at 17237_at 17300_at 17319_at 17322_at 17332_s_at 17381_at 17388_at 17392_s_at 17408_at 17424_at 17429_s_at 17457_at 17458_at 17466_s_at 17477_s_at 17482_s_at 17538_s_at 17546_s_at 17562_at 17581_g_at 17627_at 17631_at 17632_at 17645_s_at 17672_at 17675_at 17677_at 17693_at 17732_at 17743_at 17748_at 17775_at 17782_at 17841_at 17852_g_at 17900_s_at 17901_at 17911_at 17921_s_at 17922_at 17933_at 17967_at 17970_i_at 17978_s_at 17999_at 18001_at 18004_at 18012_s_at 18040_s_at 18176_at 18194_i_at 18197_at 18198_at 18213_at 18219_at 18222_at 18231_at 18232_at 18241_at 18269_s_at 18272_at 18282_at 18298_at 18316_at 18317_at 18331_s_at 18347_s_at 18383_at 18390_at 18455_at 18465_s_at 18544_at 18555_at 18556_at 18560_at 18561_at 18571_at 18588_at 18597_at 18601_s_at 18611_at 18623_at 18635_at 18659_at 18660_s_at 18673_at 18694_s_at 18705_at 18708_at 18738_f_at 18750_f_at 18778_at 18829_at 18835_at 18866_at 18875_s_at 18885_at 18887_at 18888_at 18889_at 18901_at 18907_s_at 18917_i_at 18939_at 18947_i_at 18949_at 18954_at 18959_at 18974_at 18976_at 18980_at 18989_s_at 19019_i_at 19049_at 19083_at 19130_at 19156_s_at 19178_at 19190_g_at 19199_at 19202_at 19209_s_at 19211_at 19218_at 19229_at 19322_at 19326_at 19359_s_at 19367_at 19384_at 19389_at 19397_at 19406_at 19426_s_at 19441_s_at 19442_at 19470_at 19489_s_at 19562_at 19577_at 19589_s_at 19597_s_at 19611_s_at 19624_at 19657_s_at 19667_at 19671_at 19677_at 19686_at 19689_at 19698_at 19700_s_at 19707_s_at 19708_at 19713_at 19718_at 19744_at 19836_at 19839_at 19840_s_at 19845_g_at 19854_at 19855_at 19860_at 19866_at 19871_at 19875_s_at 19879_s_at 19881_at 19913_at 19939_at 19945_at 19947_at 19951_at 19956_at 19971_at 19976_at 19998_at 20003_s_at 20015_at 20027_at 20051_at 20068_at 20093_i_at 20117_at 20150_at 20156_at 20165_at 20257_at 20262_at 20275_at 20282_s_at 20288_g_at 20293_at 20315_i_at 20330_s_at 20360_at 20363_at 20369_s_at 20384_at 20393_at 20396_at 20412_s_at 20413_at 20432_at 20433_at 20456_at 20462_at 20471_at 20511_at 20515_s_at 20517_at 20518_at 20529_at 20536_s_at 20538_s_at 20539_s_at 20576_at 20582_s_at 20586_i_at 20608_s_at 20649_at 20651_at 20684_at 20685_at 20699_at 20705_at 20715_at

TABLE 5 2X UP COLD 3 HR, ONLY 12117_at 12145_s_at 12151_at 12163_at 12187_at 12256_at 12315_at 12349_s_at 12353_at 12359_s_at 12544_at 12602_at 12610_at 12676_s_at 12686_s_at 12701_i_at 12702_at 12719_f_at 12736_f_at 12754_g_at 12766_at 12767_at 12768_at 12773_at 12788_at 12879_s_at 12891_at 12947_at 12966_s_at 12974_at 12994_s_at 13002_at 13100_at 13140_at 13167_at 13172_s_at 13179_at 13187_i_at 13219_s_at 13260_s_at 13278_f_at 13279_s_at 13285_s_at 13288_s_at 13292_s_at 13297_s_at 13351_at 13352_at 13435_at 13467_at 13488_at 13495_s_at 13656_at 13671_s_at 13691_s_at 13785_at 13803_at 13825_s_at 13904_s_at 14013_at 14021_r_at 14028_at 14064_at 14126_s_at 14145_at 14170_at 14196_at 14250_r_at 14298_g_at 14303_s_at 14339_at 14527_at 14534_s_at 14554_at 14595_at 14635_s_at 14679_s_at 14691_at 14697_g_at 14709_at 14728_s_at 14809_at 14896_at 14965_at 14984_s_at 15046_s_at 15083_at 15096_at 15105_s_at 15115_f_at 15116_f_at 15122_s_at 15126_s_at 15131_s_at 15132_s_at 15137_s_at 15153_s_at 15159_s_at 15160_s_at 15197_s_at 15355_s_at 15379_at 15417_s_at 15422_at 15451_at 15452_at 15453_s_at 15489_at 15518_at 15588_s_at 15613_s_at 15614_s_at 15616_s_at 15639_s_at 15641_s_at 15660_s_at 15687_f_at 15694_s_at 15862_at 15868_at 15878_at 15901_at 16034_at 16039_s_at 16040_at 16042_s_at 16047_at 16062_s_at 16087_s_at 16117_s_at 16118_s_at 16162_s_at 16184_at 16222_at 16250_at 16411_s_at 16442_s_at 16465_at 16486_at 16488_at 16489_at 16517_at 16571_s_at 16605_s_at 16610_s_at 16620_s_at 16636_s_at 16650_s_at 16805_s_at 16845_at 16899_at 16914_s_at 16943_s_at 16996_s_at 17010_s_at 17043_s_at 17068_s_at 17109_s_at 17128_s_at 17237_at 17319_at 17392_s_at 17429_s_at 17477_s_at 17538_s_at 17581_g_at 17627_at 17672_at 17693_at 17782_at 17841_at 17900_s_at 17933_at 17978_s_at 18001_at 18012_s_at 18198_at 18219_at 18241_at 18269_s_at 18272_at 18282_at 18298_at 18383_at 18556_at 18588_at 18601_s_at 18611_at 18694_s_at 18708_at 18738_f_at 18778_at 18829_at 18835_at 18866_at 18875_s_at 18888_at 18907_s_at 18917_i_at 18939_at 18974_at 19190_g_at 19199_at 19202_at 19211_at 19384_at 19406_at 19426_s_at 19442_at 19470_at 19577_at 19597_s_at 19624_at 19657_s_at 19667_at 19845_g_at 19855_at 19866_at 19945_at 19951_at 19998_at 20003_s_at 20015_at 20051_at 20093_i_at 20117_at 20288_g_at 20360_at 20369_s_at 20384_at 20462_at 20471_at 20515_s_at 20538_s_at 20576_at 20608_s_at 20651_at 20685_at 20705_at

TABLE 6 2X DOWN COLD, ONLY 11991_g_at 11992_at 12001_at 12006_s_at 12007_at 12009_at 12022_at 12023_s_at 12026_at 12037_at 12052_at 12125_at 12143_at 12149_at 12156_at 12166_i_at 12167_at 12169_i_at 12176_at 12179_at 12196_at 12198_at 12200_at 12202_at 12212_at 12214_g_at 12224_at 12226_at 12233_at 12240_at 12253_g_at 12270_at 12278_at 12284_at 12287_s_at 12293_at 12294_s_at 12300_at 12312_at 12315_at 12324_i_at 12331_s_at 12344_at 12348_at 12353_at 12372_at 12374_i_at 12405_at 12408_at 12410_g_at 12419_at 12427_at 12438_at 12450_s_at 12474_at 12491_at 12497_at 12500_s_at 12515_at 12521_at 12523_at 12526_at 12527_at 12534_g_at 12549_s_at 12550_s_at 12552_at 12555_s_at 12556_at 12575_s_at 12576_s_at 12581_s_at 12587_at 12597_at 12606_at 12609_at 12646_at 12649_at 12653_at 12661_at 12666_at 12678_i_at 12705_f_at 12736_f_at 12737_f_at 12758_at 12760_g_at 12764_f_at 12765_at 12772_at 12776_at 12784_at 12793_at 12794_at 12795_at 12809_g_at 12812_at 12815_at 12816_at 12818_at 12824_s_at 12828_s_at 12842_s_at 12846_s_at 12858_at 12869_s_at 12881_s_at 12889_s_at 12901_s_at 12902_at 12904_s_at 12905_s_at 12908_s_at 12910_s_at 12916_s_at 12923_s_at 12926_s_at 12931_s_at 12937_r_at 12941_g_at 12942_at 12949_at 12953_at 12958_at 12959_at 12966_s_at 12975_at 12983_at 12984_at 13002_at 13009_i_at 13011_at 13014_at 13024_at 13034_s_at 13041_s_at 13048_s_at 13067_s_at 13068_at 13073_s_at 13078_s_at 13079_at 13081_s_at 13083_at 13090_at 13092_s_at 13098_at 13103_at 13105_at 13107_s_at 13108_at 13114_at 13118_f_at 13123_at 13124_at 13133_s_at 13135_s_at 13139_at 13146_s_at 13151_g_at 13160_at 13161_at 13162_at 13165_at 13166_at 13185_at 13193_s_at 13211_s_at 13213_s_at 13219_s_at 13233_at 13236_s_at 13239_s_at 13241_s_at 13254_s_at 13266_s_at 13273_s_at 13275_f_at 13276_s_at 13278_f_at 13280_s_at 13285_s_at 13296_s_at 13347_at 13355_at 13361_at 13404_at 13406_at 13459_at 13460_at 13464_at 13523_s_at 13529_at 13541_at 13545_s_at 13550_at 13552_at 13556_i_at 13561_at 13563_s_at 13567_at 13568_at 13571_at 13576_at 13583_at 13598_at 13601_at 13604_at 13613_at 13616_s_at 13618_s_at 13619_at 13621_g_at 13623_r_at 13629_s_at 13631_at 13635_at 13646_at 13650_at 13652_at 13653_at 13655_at 13657_at 13666_s_at 13667_s_at 13669_s_at 13670_s_at 13672_s_at 13678_s_at 13679_s_at 13688_s_at 13690_s_at 13691_s_at 13692_s_at 13714_at 13724_at 13748_at 13751_at 13759_at 13767_at 13789_at 13876_at 13880_s_at 13883_at 13887_s_at 13895_at 13906_s_at 13919_at 13923_at 13932_at 13935_at 13940_at 13949_s_at 13954_g_at 13973_at 13983_at 13989_at 14010_at 14014_at 14015_s_at 14016_s_at 14025_s_at 14027_at 14030_at 14044_at 14056_at 14057_at 14061_at 14067_at 14068_s_at 14072_at 14074_at 14075_at 14083_at 14084_at 14089_at 14095_s_at 14096_at 14100_at 14101_at 14103_at 14121_at 14129_s_at 14133_s_at 14143_at 14148_at 14162_at 14194_at 14208_at 14217_at 14223_at 14235_at 14236_at 14251_f_at 14252_f_at 14285_at 14301_s_at 14316_at 14366_at 14369_at 14392_g_at 14421_at 14431_at 14436_at 14448_at 14450_at 14454_at 14459_at 14478_at 14482_at 14485_at 14492_s_at 14505_at 14510_at 14517_at 14519_at 14534_s_at 14538_r_at 14558_at 14559_s_at 14572_at 14584_at 14587_at 14595_at 14602_at 14603_at 14605_at 14620_s_at 14626_s_at 14630_s_at 14637_s_at 14640_s_at 14642_f_at 14650_s_at 14654_s_at 14667_s_at 14668_s_at 14669_s_at 14672_s_at 14673_s_at 14675_s_at 14679_s_at 14681_g_at 14682_i_at 14689_at 14701_s_at 14703_at 14712_s_at 14713_s_at 14715_s_at 14734_s_at 14781_at 14800_at 14856_s_at 14882_at 14908_at 14912_at 14914_at 14924_at 14942_at 14945_at 14955_at 14957_s_at 14974_at 14980_at 14981_at 14995_at 15009_at 15018_at 15024_at 15026_at 15047_at 15054_at 15056_at 15058_s_at 15063_at 15066_at 15081_at 15091_at 15097_s_at 15102_s_at 15107_s_at 15118_s_at 15127_s_at 15130_s_at 15132_s_at 15133_s_at 15139_s_at 15143_s_at 15146_s_at 15150_s_at 15161_s_at 15162_s_at 15167_s_at 15170_s_at 15171_s_at 15178_s_at 15182_s_at 15185_s_at 15188_s_at 15193_s_at 15196_s_at 15201_f_at 15206_s_at 15207_s_at 15213_s_at 15243_at 15256_at 15348_at 15350_at 15372_at 15383_at 15384_at 15385_at 15387_at 15406_at 15423_at 15431_at 15464_at 15468_at 15471_at 15475_s_at 15485_at 15505_at 15512_at 15514_at 15515_r_at 15529_at 15534_f_at 15538_at 15541_at 15543_at 15551_at 15574_s_at 15576_s_at 15577_s_at 15578_s_at 15581_s_at 15583_s_at 15591_s_at 15595_s_at 15602_f_at 15606_s_at 15608_s_at 15616_s_at 15618_s_at 15620_s_at 15627_s_at 15634_s_at 15637_s_at 15642_s_at 15643_s_at 15646_s_at 15651_f_at 15652_s_at 15667_s_at 15668_s_at 15670_s_at 15671_s_at 15675_s_at 15679_s_at 15685_s_at 15688_s_at 15689_s_at 15692_s_at 15775_at 15776_at 15845_at 15848_at 15858_at 15866_s_at 15894_at 15900_at 15901_at 15902_at 15913_at 15928_at 15940_at 15948_s_at 15956_at 15976_at 15978_at 15986_s_at 16004_s_at 16015_at 16017_at 16019_at 16024_at 16031_at 16055_s_at 16059_s_at 16065_s_at 16066_s_at 16069_s_at 16074_s_at 16076_s_at 16077_s_at 16084_s_at 16089_s_at 16102_s_at 16103_s_at 16105_s_at 16108_s_at 16112_s_at 16117_s_at 16118_s_at 16125_s_at 16127_s_at 16134_s_at 16136_s_at 16138_s_at 16140_s_at 16143_s_at 16144_s_at 16145_s_at 16148_s_at 16151_s_at 16158_f_at 16160_f_at 16168_s_at 16169_s_at 16171_s_at 16172_s_at 16222_at 16232_s_at 16242_at 16288_at 16294_s_at 16325_at 16346_s_at 16357_at 16380_at 16382_at 16385_s_at 16393_s_at 16402_s_at 16417_s_at 16442_s_at 16446_at 16448_g_at 16453_s_at 16457_s_at 16470_s_at 16481_s_at 16510_at 16512_s_at 16514_at 16516_at 16523_s_at 16526_at 16528_at 16531_s_at 16535_s_at 16537_s_at 16543_s_at 16544_s_at 16550_s_at 16559_s_at 16567_s_at 16577_s_at 16579_s_at 16580_s_at 16583_s_at 16584_s_at 16593_s_at 16598_s_at 16603_s_at 16604_s_at 16611_s_at 16614_s_at 16617_s_at 16618_s_at 16620_s_at 16631_s_at 16634_s_at 16639_s_at 16640_s_at 16652_s_at 16654_at 16777_at 16784_at 16811_at 16893_at 16894_at 16899_at 16920_at 16921_at 16924_s_at 16926_s_at 16931_s_at 16934_s_at 16937_at 16938_at 16942_at 16949_s_at 16950_s_at 16952_s_at 16962_s_at 16965_s_at 16970_s_at 16977_at 16984_at 16989_at 16993_at 16997_at 17000_at 17005_at 17010_s_at 17017_s_at 17031_s_at 17040_s_at 17053_s_at 17056_s_at 17063_s_at 17070_s_at 17074_s_at 17084_s_at 17085_s_at 17087_s_at 17092_s_at 17095_s_at 17096_s_at 17097_s_at 17103_s_at 17105_s_at 17110_s_at 17115_s_at 17116_s_at 17119_s_at 17122_s_at 17207_at 17215_at 17247_at 17254_at 17286_at 17288_s_at 17292_at 17303_s_at 17305_at 17318_at 17323_at 17374_at 17405_at 17415_at 17418_s_at 17420_at 17423_s_at 17426_at 17427_at 17430_s_at 17431_at 17439_g_at 17442_i_at 17449_s_at 17462_s_at 17463_at 17465_at 17475_at 17479_at 17495_s_at 17508_s_at 17522_s_at 17523_s_at 17529_s_at 17537_s_at 17539_s_at 17543_s_at 17555_s_at 17557_s_at 17560_s_at 17564_s_at 17565_s_at 17568_at 17570_g_at 17573_at 17577_g_at 17578_at 17579_s_at 17585_s_at 17596_at 17600_s_at 17823_s_at 17840_s_at 17849_s_at 17857_at 17865_at 17882_at 17885_at 17902_s_at 17910_at 17916_at 17917_s_at 17918_at 17926_s_at 17935_at 17956_i_at 17961_at 17966_at 17978_s_at 17986_s_at 17993_at 17998_s_at 18003_at 18005_at 18010_s_at 18013_r_at 18023_s_at 18029_g_at 18030_i_at 18045_at 18046_s_at 18059_i_at 18064_r_at 18065_r_at 18074_at 18076_s_at 18077_at 18078_at 18081_at 18083_r_at 18085_r_at 18091_at 18154_s_at 18165_at 18174_at 18221_at 18226_s_at 18230_at 18237_at 18255_at 18257_at 18258_s_at 18274_s_at 18275_at 18278_at 18283_at 18290_at 18291_at 18299_s_at 18300_at 18306_at 18327_s_at 18337_s_at 18339_at 18365_s_at 18402_at 18439_s_at 18487_at 18508_s_at 18512_at 18543_at 18552_at 18567_at 18573_at 18580_at 18581_at 18584_at 18587_s_at 18590_at 18591_at 18592_s_at 18600_at 18601_s_at 18607_s_at 18610_s_at 18611_at 18616_at 18622_g_at 18628_at 18631_at 18636_at 18638_at 18652_at 18657_at 18667_at 18675_at 18684_at 18686_s_at 18688_s_at 18693_s_at 18698_s_at 18706_s_at 18707_at 18726_s_at 18727_at 18732_i_at 18735_s_at 18736_at 18738_f_at 18747_f_at 18754_at 18782_at 18789_at 18806_s_at 18814_at 18823_s_at 18844_at 18859_at 18864_at 18880_at 18883_g_at 18886_at 18892_s_at 18909_s_at 18911_at 18913_s_at 18916_s_at 18921_g_at 18950_at 18951_s_at 18956_at 18966_at 18972_at 18994_at 19030_at 19039_at 19068_i_at 19108_at 19115_at 19117_s_at 19122_at 19125_s_at 19127_at 19135_at 19144_at 19157_s_at 19158_at 19177_at 19192_at 19198_at 19222_at 19226_g_at 19227_at 19230_at 19232_s_at 19263_at 19285_at 19332_at 19346_at 19347_at 19361_s_at 19362_at 19363_at 19364_at 19365_s_at 19373_at 19379_at 19381_at 19382_at 19401_at 19402_at 19406_at 19413_at 19416_at 19429_at 19432_s_at 19439_at 19448_s_at 19454_at 19462_s_at 19464_at 19469_at 19483_at 19484_s_at 19513_at 19548_at 19563_s_at 19567_at 19581_at 19595_s_at 19606_at 19623_at 19627_s_at 19636_at 19641_at 19652_at 19655_at 19658_at 19660_at 19665_s_at 19667_at 19690_s_at 19695_at 19717_at 19726_s_at 19752_s_at 19759_at 19782_at 19789_s_at 19803_s_at 19828_at 19831_i_at 19833_s_at 19834_at 19835_at 19841_at 19867_at 19870_s_at 19871_at 19872_at 19876_at 19897_s_at 19903_at 19905_at 19906_at 19907_at 19910_at 19920_s_at 19932_at 19951_at 19962_at 19963_at 19969_at 19970_s_at 19972_at 19981_at 19990_at 19996_at 19999_s_at 20009_s_at 20013_at 20017_at 20018_at 20024_s_at 20045_at 20047_at 20048_at 20050_at 20051_at 20058_at 20067_at 20069_at 20099_at 20100_at 20113_s_at 20123_at 20127_s_at 20129_at 20133_i_at 20152_at 20154_at 20173_at 20178_s_at 20183_at 20188_at 20189_at 20197_at 20200_at 20210_g_at 20213_at 20229_at 20232_s_at 20255_at 20278_s_at 20284_at 20288_g_at 20294_at 20312_s_at 20331_at 20335_s_at 20350_s_at 20354_s_at 20355_at 20369_s_at 20378_g_at 20383_at 20385_s_at 20387_at 20399_at 20409_g_at 20420_at 20429_s_at 20439_at 20440_at 20444_at 20445_at 20449_at 20474_at 20480_s_at 20495_s_at 20499_at 20501_at 20516_at 20520_s_at 20530_s_at 20538_s_at 20547_at 20558_at 20561_at 20567_at 20571_at 20590_at 20592_at 20594_at 20608_s_at 20612_s_at 20616_at 20620_g_at 20635_s_at 20637_at 20643_at 20654_s_at 20670_at 20674_s_at 20684_at 20685_at 20689_s_at 20693_at 20701_s_at 20704_at 20707_s_at 20719_at

TABLE 7 SALINE STRESS RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 2227 12011_S_AT 2228 12153_AT 2229 12180_AT 2230 12186_AT 2231 12216_AT 2232 12265_AT 2233 12335_AT 2234 12449_S_AT 2235 12470_AT 2236 12479_AT 2237 12487_AT 2238 12493_G_AT 2239 12562_AT 2240 12685_AT 2241 12704_F_AT 2242 12709_F_AT 2243 12734_F_AT 2244 12739_S_AT 2245 12750_S_AT 2246 12761_S_AT 2247 12813_AT 2248 12845_S_AT 2249 12946_AT 2250 13003_S_AT 2251 13052_S_AT 2252 13094_AT 2253 13142_AT 2254 13172_S_AT 17880_S_AT 2255 13198_I_AT 2256 13209_S_AT 16165_S_AT 2257 13229_S_AT 2258 13253_F_AT 2259 13344_S_AT 2260 13370_AT 2261 13387_AT 2262 13408_S_AT 2263 13429_AT 2264 13472_AT 2265 13526_AT 2266 13569_AT 2267 13614_AT 2268 13686_S_AT 2269 13718_AT 2270 13719_AT 2271 13902_AT 2272 13918_AT 2273 13944_AT 2274 13964_AT 2275 13993_S_AT 2276 14000_AT 2277 14003_AT 2278 14032_AT 2279 14043_AT 2280 14070_AT 2281 14267_AT 2282 14269_AT 2283 14418_AT 2284 14427_AT 2285 14501_AT 2286 14544_AT 2287 14546_S_AT 2288 14570_AT 2289 14596_AT 2290 14729_S_AT 2291 14874_AT 2292 14888_AT 2293 14951_AT 2294 14952_AT 2295 14959_AT 2296 14979_AT 2297 15006_AT 2298 15042_AT 2299 15049_AT 2300 15062_AT 2301 15108_S_AT 2302 15147_S_AT 2303 15175_S_AT 2304 15176_S_AT 2305 15186_S_AT 18696_S_AT 2306 15192_S_AT 2307 15208_S_AT 2308 15324_AT 2309 15371_AT 2310 15424_AT 2311 15463_AT 2312 15465_AT 2313 15497_S_AT 2314 15589_S_AT 2315 15636_S_AT 2316 15663_S_AT 2317 15770_AT 2318 15792_AT 2319 15855_AT 2320 15860_AT 2321 15891_AT 2322 15898_AT 2323 15909_AT 2324 15965_AT 2325 15969_S_AT 2326 15975_S_AT 2327 15995_S_AT 2328 15998_S_AT 18090_S_AT 2329 16028_AT 2330 16050_AT 2331 16060_S_AT 2332 16067_S_AT 2333 16072_S_AT 2334 16088_F_AT 2335 16273_AT 2336 16314_AT 2337 16413_S_AT 2338 16414_AT 2339 16426_AT 2340 16436_AT 2341 16455_AT 2342 16502_AT 2343 16548_S_AT 2344 16568_S_AT 2345 16582_S_AT 2346 16589_S_AT 2347 16594_S_AT 2348 16613_S_AT 2349 16651_S_AT 2350 16668_AT 2351 16820_AT 2352 16987_S_AT 2353 16995_AT 2354 17039_S_AT 2355 17273_AT 2356 17278_AT 2357 17433_AT 2358 17467_AT 2359 17566_AT 2360 17595_S_AT 2361 17744_S_AT 2362 17758_AT 2363 17864_AT 2364 17868_AT 2365 17876_AT 2366 17894_AT 2367 17942_S_AT 2368 18008_R_AT 2369 18027_AT 2370 18053_S_AT 2371 18062_AT 2372 18082_AT 2373 18121_S_AT 2374 18240_S_AT 2375 18248_S_AT 2376 18264_AT 2377 18276_AT 2378 18287_AT 2379 18310_AT 2380 18367_S_AT 2381 18506_AT 2382 18605_S_AT 2383 18618_S_AT 2384 18626_AT 2385 18666_S_AT 2386 18834_AT 2387 18847_AT 2388 18896_AT 2389 18899_S_AT 2390 18973_AT 2391 18983_S_AT 2392 18988_AT 2393 18998_S_AT 2394 19065_AT 2395 19119_I_AT 19121_AT 2396 19207_AT 2397 19220_AT 2398 19284_AT 2399 19315_AT 2400 19348_AT 2401 19403_S_AT 2402 19437_S_AT 2403 19502_AT 2404 19609_AT 2405 19645_AT 2406 19742_AT 2407 19863_AT 2408 19873_AT 2409 19891_AT 2410 20004_S_AT 2411 20053_AT 2412 20138_AT 2413 20193_AT 2414 20199_AT 2415 20220_AT 2416 20239_G_AT 2417 20297_AT 2418 20324_S_AT 2419 20353_AT 2420 20362_AT 2421 20389_AT 2422 20546_AT 2423 20600_AT 2424 20623_AT 2425 20629_AT 2426 20648_S_AT 2427 20668_AT

TABLE 8 2X UP IN SALT, ONLY 12037_at 12137_at 12153_at 12186_at 12216_at 12268_at 12449_s_at 12470_at 12476_at 12487_at 12493_g_at 12609_at 12685_at 12704_f_at 12709_f_at 12734_f_at 12739_s_at 12750_s_at 12761_s_at 12819_at 12845_s_at 12946_at 13142_at 13198_i_at 13229_s_at 13275_f_at 13344_s_at 13370_at 13408_s_at 13464_at 13472_at 13526_at 13614_at 13652_at 13679_s_at 13751_at 13918_at 13919_at 13944_at 13964_at 13987_s_at 13993_s_at 14000_at 14032_at 14043_at 14052_at 14067_at 14070_at 14269_at 14285_at 14427_at 14501_at 14540_at 14570_at 14578_s_at 14596_at 14646_s_at 14662_f_at 14668_s_at 14729_s_at 14874_at 14888_at 14918_at 14952_at 14959_at 14986_at 15006_at 15042_at 15047_at 15062_at 15063_at 15108_s_at 15133_s_at 15147_s_at 15170_s_at 15175_s_at 15182_s_at 15190_s_at 15192_s_at 15324_at 15392_at 15424_at 15467_at 15497_s_at 15581_s_at 15623_f_at 15636_s_at 15646_s_at 15670_s_at 15770_at 15775_at 15778_at 15792_at 15855_at 15891_at 15909_at 15923_at 15969_s_at 15975_s_at 15995_s_at 15998_s_at 16017_at 16050_at 16067_s_at 16072_s_at 16165_s_at 16190_at 16196_at 16273_at 16314_at 16413_s_at 16414_at 16417_s_at 16455_at 16548_s_at 16582_s_at 16589_s_at 16594_s_at 16613_s_at 16651_s_at 16668_at 16690_g_at 16762_at 16820_at 16873_i_at 16987_s_at 16989_at 16995_at 17039_s_at 17040_s_at 17400_s_at 17425_s_at 17433_at 17467_at 17490_s_at 17529_s_at 17543_s_at 17566_at 17595_s_at 17744_s_at 17758_at 17855_at 17864_at 17876_at 18008_r_at 18013_r_at 18024_s_at 18027_at 18053_s_at 18078_at 18082_at 18090_s_at 18091_at 18121_s_at 18264_at 18276_at 18300_at 18367_s_at 18471_at 18506_at 18605_s_at 18626_at 18666_s_at 18747_f_at 18782_at 18834_at 18847_at 18913_s_at 18973_at 18988_at 18998_s_at 19065_at 19068_i_at 19123_at 19177_at 19220_at 19284_at 19288_at 19315_at 19437_s_at 19484_s_at 19502_at 19503_at 19592_at 19645_at 19742_at 19835_at 19873_at 19891_at 19992_at 20004_s_at 20053_at 20133_i_at 20138_at 20190_at 20199_at 20200_at 20297_at 20324_s_at 20335_s_at 20353_at 20362_at 20385_s_at 20389_at 20402_s_at 20450_at 20468_at 20489_at 20546_at 20569_s_at 20600_at 20623_at 20648_s_at 20678_at 20686_at 20707_s_at

TABLE 9 2X UP SALT, 3 HR ONLY 12037_at 12137_at 12153_at 12186_at 12216_at 12268_at 12470_at 12476_at 12487_at 12493_g_at 12609_at 12685_at 12704_f_at 12709_f_at 12734_f_at 12739_s_at 12750_s_at 12819_at 12946_at 13142_at 13229_s_at 13275_f_at 13370_at 13408_s_at 13464_at 13472_at 13614_at 13652_at 13679_s_at 13918_at 13919_at 13944_at 13987_s_at 13993_s_at 14000_at 14032_at 14043_at 14052_at 14067_at 14269_at 14285_at 14501_at 14540_at 14570_at 14596_at 14668_s_at 14729_s_at 14888_at 14918_at 14952_at 14959_at 14986_at 15006_at 15042_at 15047_at 15062_at 15063_at 15108_s_at 15133_s_at 15147_s_at 15170_s_at 15175_s_at 15182_s_at 15190_s_at 15192_s_at 15324_at 15424_at 15467_at 15497_s_at 15623_f_at 15636_s_at 15646_s_at 15670_s_at 15770_at 15775_at 15778_at 15792_at 15855_at 15891_at 15909_at 15923_at 15969_s_at 15975_s_at 15995_s_at 15998_s_at 16017_at 16050_at 16067_s_at 16072_s_at 16165_s_at 16196_at 16273_at 16314_at 16414_at 16417_s_at 16455_at 16548_s_at 16582_s_at 16589_s_at 16594_s_at 16613_s_at 16651_s_at 16668_at 16762_at 16820_at 16873_i_at 16987_s_at 16989_at 17039_s_at 17040_s_at 17425_s_at 17433_at 17490_s_at 17543_s_at 17744_s_at 17864_at 17876_at 18008_r_at 18013_r_at 18024_s_at 18027_at 18053_s_at 18078_at 18082_at 18090_s_at 18091_at 18121_s_at 18264_at 18276_at 18367_s_at 18471_at 18506_at 18605_s_at 18626_at 18666_s_at 18747_f_at 18782_at 18834_at 18847_at 18913_s_at 18973_at 18988_at 19065_at 19068_i_at 19123_at 19177_at 19220_at 19288_at 19315_at 19437_s_at 19484_s_at 19502_at 19503_at 19592_at 19645_at 19742_at 19835_at 19873_at 19891_at 20004_s_at 20053_at 20133_i_at 20138_at 20190_at 20199_at 20200_at 20220_at 20362_at 20385_s_at 20389_at 20489_at 20546_at 20623_at 20648_s_at 20678_at 20707_s_at

TABLE 10 2X DOWN SALT, ONLY 12011_s_at 12180_at 12265_at 12335_at 12479_at 12562_at 12656_at 12813_at 13003_s_at 13052_s_at 13094_at 13178_at 13253_f_at 13387_at 13429_at 13472_at 13569_at 13686_s_at 13718_at 13719_at 13902_at 14003_at 14144_at 14267_at 14418_at 14544_at 14546_s_at 14636_s_at 14951_at 14956_s_at 14979_at 14990_at 15040_g_at 15049_at 15115_f_at 15137_s_at 15148_s_at 15176_s_at 15208_s_at 15371_at 15453_s_at 15463_at 15465_at 15589_s_at 15663_s_at 15860_at 15898_at 15931_at 15965_at 15970_s_at 15972_s_at 16005_s_at 16028_at 16046_s_at 16060_s_at 16088_f_at 16150_s_at 16166_s_at 16316_at 16340_at 16367_i_at 16426_at 16427_at 16436_at 16489_at 16502_at 16568_s_at 16638_s_at 16646_s_at 17273_at 17278_at 17567_at 17868_at 17880_s_at 17894_at 17901_at 17942_s_at 17960_at 17999_at 18062_at 18240_s_at 18248_s_at 18267_at 18279_s_at 18287_at 18310_at 18351_s_at 18455_at 18560_at 18571_at 18618_s_at 18896_at 18899_s_at 18967_s_at 18983_s_at 19119_i_at 19121_at 19207_at 19348_at 19403_s_at 19609_at 19742_at 19826_at 19863_at 19883_at 20193_at 20239_g_at 20433_at 20629_at 20668_at

TABLE 11 OSMOTIC STRESS RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 2428 11994_AT 2429 12028_AT 2430 12033_AT 2431 12039_AT 2432 12068_AT 2433 12096_AT 2434 12110_AT 2435 12114_AT 2436 12135_AT 2437 12139_AT 2438 12189_AT 2439 12191_AT 2440 12211_AT 2441 12223_S_AT 2442 12366_S_AT 12869_S_AT 2443 12381_AT 2444 12406_S_AT 2445 12412_AT 2446 12453_AT 2447 12571_S_AT 2448 12662_AT 2449 12746_I_AT 2450 12774_AT 2451 12787_AT 2452 12847_AT 2453 12848_AT 2454 12895_AT 2455 12911_S_AT 2456 12920_AT 12921_S_AT 2457 13027_AT 2458 13059_AT 2459 13075_I_AT 2460 13180_S_AT 2461 13255_I_AT 2462 13270_AT 18167_S_AT 2463 13283_S_AT 2464 13382_AT 2465 13386_S_AT 2466 13433_AT 2467 13482_AT 2468 13732_AT 2469 13733_I_AT 2470 13842_AT 2471 13860_S_AT 2472 13868_AT 2473 13901_AT 2474 13933_AT 2475 13995_AT 2476 14062_AT 2477 14118_I_AT 2478 14141_AT 2479 14310_AT 2480 14354_AT 2481 14476_AT 2482 14513_S_AT 2483 14568_S_AT 2484 14604_AT 2485 14634_S_AT 2486 14660_S_AT 2487 14666_S_AT 2488 14686_S_AT 17464_AT 2489 14726_S_AT 2490 14848_S_AT 2491 14873_AT 2492 14883_AT 2493 15082_AT 2494 15121_S_AT 16014_S_AT 2495 15168_S_AT 2496 15271_AT 2497 15338_AT 2498 15418_AT 2499 15429_AT 2500 15548_AT 2501 15666_S_AT 2502 15672_S_AT 2503 15680_S_AT 2504 15867_AT 2505 15918_AT 2506 15999_S_AT 2507 16303_AT 2508 16363_AT 2509 16440_S_AT 2510 16458_S_AT 2511 16475_AT 2512 16513_S_AT 2513 16529_AT 2514 16547_S_AT 2515 16553_F_AT 2516 16563_S_AT 2517 16629_S_AT 2518 16797_AT 2519 16814_AT 2520 16832_AT 2521 16976_S_AT 2522 17007_AT 2523 17037_S_AT 2524 17054_S_AT 2525 17257_S_AT 18725_S_AT 2526 17270_AT 2527 17275_I_AT 2528 17376_AT 2529 17378_AT 2530 17468_AT 2531 17481_AT 2532 17511_S_AT 2533 17519_S_AT 2534 17815_S_AT 2535 17897_AT 2536 17923_S_AT 2537 17934_AT 2538 17937_S_AT 2539 17944_AT 2540 17958_AT 2541 18216_AT 2542 18227_AT 2543 18284_AT 2544 18301_S_AT 2545 18312_S_AT 2546 18326_S_AT 2547 18369_AT 2548 18411_AT 2549 18533_AT 2550 18576_S_AT 2551 18599_AT 2552 18640_AT 2553 18672_S_AT 2554 18720_S_AT 2555 18768_AT 2556 18877_AT 2557 18942_AT 2558 18945_AT 2559 18960_AT 2560 18965_AT 2561 19060_AT 2562 19164_G_AT 2563 19266_AT 2564 19366_S_AT 2565 19369_AT 2566 19371_AT 2567 19386_AT 2568 19412_AT 2569 19427_S_AT 2570 19622_G_AT 2571 19681_AT 2572 19819_S_AT 2573 19961_S_AT 2574 20002_AT 2575 20034_I_AT 2576 20062_AT 2577 20136_AT 2578 20223_AT 2579 20235_I_AT 2580 20401_AT 2581 20407_AT 2582 20470_AT 2583 20626_AT 2584 20631_S_AT 2585 20647_AT

TABLE 12 2X UP IN MANNITOL, ONLY 12039_at 12068_at 12139_at 12212_at 12278_at 12366_s_at 12453_at 12556_at 12575_s_at 12746_i_at 12848_at 12869_s_at 12920_at 12921_s_at 13041_s_at 13059_at 13241_s_at 13255_i_at 13270_at 13382_at 13406_at 13433_at 13550_at 13672_s_at 13716_at 13842_at 13933_at 13995_at 14062_at 14075_at 14162_at 14208_at 14217_at 14235_at 14310_at 14431_at 14513_s_at 14584_at 14604_at 14673_s_at 14856_s_at 15207_s_at 15338_at 15406_at 15418_at 15591_s_at 15666_s_at 15680_s_at 15866_s_at 15918_at 16340_at 16553_f_at 16797_at 16832_at 16993_at 17037_s_at 17054_s_at 17083_s_at 17097_s_at 17119_s_at 17270_at 17305_at 17376_at 17378_at 17449_s_at 17481_at 17533_s_at 17832_s_at 17923_s_at 17944_at 18059_i_at 18216_at 18230_at 18255_at 18284_at 18301_s_at 18312_s_at 18326_s_at 18599_at 18672_s_at 18720_s_at 18768_at 18814_at 18877_at 18921_g_at 18960_at 19060_at 19182_at 19192_at 19266_at 19369_at 19386_at 19402_at 19412_at 19432_s_at 19469_at 19622_g_at 19819_s_at 19826_at 20152_at 20223_at 20235_i_at 20365_s_at 20470_at 20537_at 20547_at

TABLE 13 2X UP IN MANNITOL, 3 HR ONLY 12039_at 12068_at 12139_at 12212_at 12278_at 12366_s_at 12453_at 12556_at 12575_s_at 12746_i_at 12848_at 12869_s_at 12920_at 12921_s_at 13041_s_at 13059_at 13241_s_at 13382_at 13406_at 13433_at 13550_at 13672_s_at 13933_at 13995_at 14062_at 14075_at 14162_at 14217_at 14310_at 14431_at 14513_s_at 14584_at 14604_at 14673_s_at 14856_s_at 15207_s_at 15338_at 15418_at 15591_s_at 15866_s_at 15918_at 16340_at 16553_f_at 16797_at 16832_at 17037_s_at 17054_s_at 17083_s_at 17097_s_at 17270_at 17305_at 17376_at 17378_at 17449_s_at 17481_at 17533_s_at 17923_s_at 17944_at 18059_i_at 18216_at 18230_at 18255_at 18301_s_at 18312_s_at 18326_s_at 18599_at 18720_s_at 18768_at 18814_at 18877_at 18921_g_at 18960_at 19060_at 19192_at 19266_at 19369_at 19386_at 19402_at 19412_at 19432_s_at 19469_at 19622_g_at 19819_s_at 20152_at 20223_at 20235_i_at 20365_s_at 20470_at 20537_at

TABLE 14 2X DOWN IN MANNITOL, ONLY 12028_at 12033_at 12110_at 12114_at 12189_at 12191_at 12211_at 12223_s_at 12268_at 12345_at 12381_at 12406_s_at 12412_at 12522_at 12571_s_at 12662_at 12787_at 12847_at 12895_at 12911_s_at 13027_at 13075_i_at 13221_at 13262_s_at 13283_s_at 13386_s_at 13447_s_at 13482_at 13634_s_at 13709_s_at 13732_at 13733_i_at 13812_s_at 13825_s_at 13860_s_at 13868_at 13901_at 14052_at 14224_at 14244_s_at 14254_s_at 14256_f_at 14354_at 14476_at 14568_s_at 14634_s_at 14646_s_at 14660_s_at 14686_s_at 14726_s_at 14848_s_at 14873_at 14883_at 14897_at 14918_at 15082_at 15084_at 15098_s_at 15105_s_at 15121_s_at 15126_s_at 15168_s_at 15271_at 15429_at 15548_at 15672_s_at 15753_at 15867_at 15999_s_at 16001_at 16021_s_at 16190_at 16260_at 16303_at 16363_at 16458_s_at 16468_at 16475_at 16513_s_at 16529_at 16563_s_at 16690_g_at 16814_at 16847_at 16927_s_at 16976_s_at 17007_at 17014_s_at 17016_s_at 17071_s_at 17090_s_at 17257_s_at 17275_i_at 17424_at 17464_at 17468_at 17511_s_at 17519_s_at 17525_s_at 17645_s_at 17741_at 17815_s_at 17897_at 17899_at 17934_at 17937_s_at 17958_at 18012_s_at 18227_at 18272_at 18331_s_at 18369_at 18411_at 18533_at 18576_s_at 18640_at 18696_s_at 18945_at 18949_at 18953_at 18965_at 19164_g_at 19322_at 19366_s_at 19371_at 19397_at 19427_s_at 19681_at 19707_s_at 19839_at 19961_s_at 19976_at 19998_at 20002_at 20034_i_at 20136_at 20382_s_at 20407_at 20529_at 20626_at 20631_s_at 20647_at 20699_at

TABLE 15 COLD & OSOMOTIC STRESS RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 1699 12040_AT 1700 12048_AT 1701 12054_S_AT 1702 12077_AT 1703 12107_I_AT 1704 12113_AT 1705 12154_AT 1706 12171_AT 1707 12212_AT 1708 12278_AT 1709 12317_AT 1710 12325_AT 1711 12333_AT 1712 12345_AT 1713 12349_S_AT 14254_S_AT 14256_F_AT 1714 12356_AT 1715 12380_AT 1716 12392_AT 1717 12460_S_AT 1718 12556_AT 1719 12575_S_AT 1720 12686_S_AT 1721 12701_I_AT 1722 12754_G_AT 1723 12782_R_AT 1724 12784_AT 1725 12879_S_AT 1726 12891_AT 16817_S_AT 1727 12898_G_AT 1728 12974_AT 1729 12998_AT 1730 13041_S_AT 1731 13124_AT 1732 13134_S_AT 1733 13144_AT 1734 13147_AT 1735 13152_S_AT 1736 13187_I_AT 16981_S_AT 1737 13192_S_AT 17525_S_AT 1738 13212_S_AT 1739 13215_S_AT 16649_S_AT 1740 13241_S_AT 1741 13246_AT 1742 13262_S_AT 1743 13286_S_AT 1744 13324_AT 1745 13340_S_AT 1746 13361_AT 1747 13406_AT 1748 13441_S_AT 1749 13513_AT 1750 13550_AT 1751 13573_AT 1752 13577_S_AT 1753 13606_AT 1754 13609_AT 1755 13625_S_AT 1756 13626_AT 1757 13634_S_AT 1758 13672_S_AT 18916_S_AT 1759 13709_S_AT 1760 13736_AT 1761 13775_AT 1762 13810_AT 1763 13812_S_AT 1764 13825_S_AT 1765 14015_S_AT 14016_S_AT 1766 14029_AT 1767 14036_AT 1768 14051_AT 1769 14060_AT 1770 14064_AT 1771 14066_AT 1772 14075_AT 1773 14094_S_AT 19999_S_AT 1774 14096_AT 1775 14104_AT 1776 14123_S_AT 1777 14126_S_AT 1778 14131_AT 1779 14136_AT 1780 14139_AT 14140_AT 1781 14162_AT 14217_AT 1782 14178_AT 1783 14201_AT 1784 14208_AT 1785 14235_AT 1786 14242_S_AT 1787 14431_AT 1788 14480_AT 1789 14497_AT 1790 14553_AT 1791 14584_AT 1792 14600_AT 1793 14673_S_AT 19432_S_AT 1794 14681_G_AT 1795 14699_AT 1796 14751_AT 1797 14762_AT 1798 14828_S_AT 1799 14856_S_AT 1800 14882_AT 1801 14897_AT 1802 14978_AT 1803 14985_S_AT 1804 15031_AT 1805 15084_AT 1806 15096_AT 1807 15105_S_AT 1808 15110_S_AT 1809 15111_S_AT 1810 15120_S_AT 1811 15126_S_AT 1812 15142_S_AT 1813 15144_S_AT 1814 15184_S_AT 1815 15198_S_AT 1816 15203_S_AT 1817 15207_S_AT 1818 15240_AT 1819 15366_AT 1820 15398_AT 1821 15406_AT 1822 15448_AT 1823 15466_AT 1824 15481_AT 1825 15484_AT 1826 15549_AT 1827 15591_S_AT 1828 15606_S_AT 1829 15614_S_AT 16927_S_AT 1830 15629_S_AT 1831 15633_S_AT 1832 15641_S_AT 18012_S_AT 1833 15720_AT 1834 15815_S_AT 1835 15817_AT 1836 15837_AT 1837 15841_AT 1838 15866_S_AT 18255_AT 1839 15872_AT 18331_S_AT 1840 15892_AT 1841 15933_AT 1842 15947_AT 1843 15959_S_AT 1844 16001_AT 1845 16052_AT 1846 16161_S_AT 1847 16204_AT 1848 16232_S_AT 1849 16252_AT 1850 16260_AT 1851 16266_AT 1852 16299_AT 1853 16365_AT 1854 16468_AT 1855 16477_AT 1856 16491_AT 1857 16523_S_AT 1858 16566_S_AT 1859 16570_S_AT 1860 16688_AT 1861 16840_AT 1862 16847_AT 1863 16893_AT 1864 16896_S_AT 1865 16898_S_AT 1866 16912_S_AT 1867 16980_AT 1868 16993_AT 1869 17008_AT 1870 17012_S_AT 1871 17014_S_AT 1872 17016_S_AT 1873 17032_S_AT 1874 17050_S_AT 17051_S_AT 1875 17071_S_AT 1876 17090_S_AT 18690_S_AT 1877 17097_S_AT 1878 17104_S_AT 1879 17119_S_AT 1880 17160_AT 1881 17305_AT 1882 17424_AT 1883 17449_S_AT 1884 17452_G_AT 1885 17540_S_AT 1886 17552_S_AT 1887 17571_AT 1888 17589_AT 1889 17641_G_AT 1890 17741_AT 18098_AT 1891 17766_AT 1892 17873_S_AT 1893 17904_AT 1894 17920_S_AT 1895 17925_AT 1896 17943_AT 1897 18059_I_AT 1898 18230_AT 1899 18263_AT 1900 18272_AT 1901 18540_AT 1902 18608_AT 1903 18647_AT 1904 18662_S_AT 1905 18664_AT 1906 18695_S_AT 1907 18704_AT 1908 18814_AT 1909 18907_S_AT 1910 18921_G_AT 1911 18924_AT 1912 18949_AT 19707_S_AT 1913 18995_AT 1914 19017_AT 1915 19034_AT 1916 19063_AT 1917 19142_AT 1918 19158_AT 1919 19180_AT 1920 19187_AT 1921 19192_AT 1922 19195_AT 1923 19199_AT 1924 19231_AT 1925 19263_AT 1926 19308_AT 1927 19322_AT 1928 19365_S_AT 1929 19372_AT 1930 19389_AT 1931 19392_AT 1932 19397_AT 1933 19400_AT 1934 19402_AT 1935 19458_AT 1936 19469_AT 1937 19473_AT 1938 19597_S_AT 1939 19710_S_AT 1940 19830_AT 1941 19839_AT 1942 19840_S_AT 1943 19853_AT 1944 19860_AT 1945 19880_AT 1946 19889_AT 1947 19898_AT 1948 19914_AT 1949 19924_AT 1950 19949_AT 1951 19976_AT 1952 19998_AT 1953 20030_AT 1954 20151_AT 1955 20152_AT 1956 20187_AT 1957 20214_I_AT 1958 20269_AT 1959 20271_AT 1960 20273_AT 1961 20299_AT 1962 20323_AT 1963 20429_S_AT 1964 20457_AT 1965 20480_S_AT 1966 20529_AT 1967 20547_AT 1968 20555_S_AT 1969 20699_AT

TABLE 16 2X UP IN MANNITOL & COLD, ONLY 12345_at 12784_at 13153_r_at 13212_s_at 13215_s_at 13246_at 13262_s_at 13361_at 13625_s_at 13764_at 13810_at 14015_s_at 14016_s_at 14060_at 14096_at 14123_s_at 14139_at 14219_at 14248_at 14254_s_at 14256_f_at 14609_at 14636_s_at 14681_g_at 14699_at 14704_s_at 14828_s_at 14882_at 15110_s_at 15184_s_at 15448_at 15629_s_at 15720_at 15846_at 15947_at 16161_s_at 16365_at 16427_at 16566_s_at 16570_s_at 16649_s_at 16688_at 16712_at 16817_s_at 16840_at 16893_at 16912_s_at 16916_s_at 16927_s_at 16981_s_at 17012_s_at 17014_s_at 17051_s_at 17066_s_at 17540_s_at 17567_at 17766_at 17904_at 17920_s_at 17943_at 18263_at 18351_s_at 18662_s_at 18670_g_at 18695_s_at 18704_at 18729_at 18995_at 19158_at 19473_at 19710_s_at 19883_at 19889_at 20030_at 20269_at 20271_at 20299_at 20429_s_at 20438_at 20480_s_at

TABLE 17 2X DOWN COLD & MANNITOL, ONLY 12040_at 12048_at 12054_s_at 12077_at 12107_i_at 12113_at 12154_at 12171_at 12317_at 12325_at 12333_at 12356_at 12380_at 12392_at 12460_s_at 12686_s_at 12701_i_at 12782_r_at 12879_s_at 12898_g_at 12974_at 12998_at 13144_at 13147_at 13152_s_at 13192_s_at 13286_s_at 13324_at 13340_s_at 13441_s_at 13513_at 13573_at 13606_at 13609_at 13626_at 13736_at 13775_at 14029_at 14036_at 14051_at 14064_at 14066_at 14094_s_at 14104_at 14126_s_at 14131_at 14136_at 14178_at 14192_at 14201_at 14242_s_at 14480_at 14497_at 14553_at 14612_at 14751_at 14762_at 14978_at 14985_s_at 15031_at 15096_at 15111_s_at 15120_s_at 15142_s_at 15198_s_at 15203_s_at 15240_at 15366_at 15392_at 15398_at 15466_at 15481_at 15484_at 15549_at 15623_f_at 15815_s_at 15817_at 15841_at 15892_at 15933_at 15959_s_at 16052_at 16204_at 16252_at 16266_at 16299_at 16477_at 16491_at 16561_s_at 16645_s_at 16898_s_at 16980_at 17008_at 17104_s_at 17160_at 17317_at 17400_s_at 17452_g_at 17477_s_at 17500_s_at 17552_s_at 17571_at 17572_s_at 17589_at 17641_g_at 17855_at 17873_s_at 17925_at 18098_at 18540_at 18608_at 18647_at 18664_at 18690_s_at 18725_s_at 18924_at 19017_at 19034_at 19063_at 19141_at 19142_at 19180_at 19187_at 19195_at 19199_at 19231_at 19308_at 19372_at 19392_at 19400_at 19458_at 19597_s_at 19762_at 19830_at 19853_at 19869_at 19880_at 19898_at 19914_at 19924_at 19949_at 20151_at 20187_at 20214_i_at 20273_at 20323_at 20457_at 20555_s_at

TABLE 18 COLD & SALINE STRESS RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 1970 12021_AT 1971 12037_AT 1972 12094_AT 1973 12098_AT 1974 12128_AT 1975 12148_AT 1976 12151_AT 1977 12357_S_AT 1978 12394_AT 1979 12472_S_AT 1980 12475_AT 1981 12482_S_AT 1982 12490_AT 1983 12505_S_AT 1984 12531_AT 1985 12540_S_AT 1986 12541_AT 1987 12577_AT 1988 12594_AT 1989 12629_AT 1990 12642_AT 1991 12656_AT 1992 12660_AT 1993 12712_F_AT 1994 12725_R_AT 1995 12745_AT 1996 12777_I_AT 1997 12790_S_AT 1998 12798_AT 1999 12801_AT 2000 12855_F_AT 2001 12887_S_AT 2002 12933_R_AT 2003 12951_AT 2004 13005_AT 2005 13015_S_AT 2006 13115_AT 2007 13178_AT 2008 13228_AT 2009 13236_S_AT 16646_S_AT 2010 13266_S_AT 15211_S_AT 2011 13275_F_AT 2012 13335_AT 2013 13362_S_AT 2014 13428_AT 2015 13464_AT 2016 13480_AT 2017 13538_AT 2018 13544_AT 2019 13549_AT 2020 13565_AT 2021 13580_AT 2022 13588_AT 2023 13649_AT 2024 13652_AT 2025 13679_S_AT 2026 13696_AT 2027 13702_S_AT 2028 13751_AT 2029 13919_AT 2030 13943_AT 2031 13950_S_AT 2032 14050_AT 2033 14055_S_AT 16166_S_AT 2034 14067_AT 2035 14078_AT 2036 14110_I_AT 2037 14144_AT 2038 14232_AT 2039 14285_AT 2040 14346_AT 2041 14432_AT 2042 14468_AT 2043 14479_AT 2044 14524_S_AT 2045 14608_AT 2046 14621_AT 2047 14635_S_AT 17128_S_AT 2048 14640_S_AT 2049 14643_S_AT 2050 14663_S_AT 2051 14668_S_AT 2052 14688_S_AT 18279_S_AT 2053 14737_S_AT 2054 14768_AT 2055 14875_AT 2056 14911_S_AT 17056_S_AT 2057 14924_AT 2058 14956_S_AT 15148_S_AT 18673_AT 2059 14964_AT 2060 15022_AT 2061 15040_G_AT 2062 15047_AT 2063 15063_AT 2064 15085_S_AT 2065 15123_S_AT 2066 15133_S_AT 2067 15137_S_AT 2068 15153_S_AT 2069 15170_S_AT 2070 15172_S_AT 2071 15182_S_AT 2072 15190_S_AT 2073 15241_S_AT 2074 15389_AT 2075 15453_S_AT 2076 15495_AT 2077 15496_AT 2078 15519_S_AT 2079 15562_AT 2080 15580_S_AT 2081 15582_S_AT 2082 15638_S_AT 18751_F_AT 2083 15646_S_AT 2084 15647_S_AT 2085 15654_S_AT 2086 15655_S_AT 2087 15658_S_AT 2088 15670_S_AT 2089 15775_AT 2090 15798_AT 2091 15930_AT 2092 15931_AT 2093 15949_S_AT 2094 16017_AT 2095 16053_I_AT 2096 16078_S_AT 2097 16086_S_AT 2098 16120_S_AT 2099 16126_S_AT 2100 16150_S_AT 2101 16159_S_AT 2102 16230_AT 2103 16306_AT 2104 16367_I_AT 2105 16417_S_AT 18083_R_AT 2106 16418_S_AT 2107 16423_AT 2108 16449_S_AT 2109 16484_S_AT 2110 16489_AT 2111 16565_S_AT 2112 16596_S_AT 2113 16600_S_AT 2114 16603_S_AT 2115 16638_S_AT 2116 16642_S_AT 2117 16763_AT 2118 16914_S_AT 2119 16968_AT 2120 16983_AT 2121 16989_AT 2122 17002_AT 2123 17015_S_AT 2124 17040_S_AT 18913_S_AT 2125 17232_AT 2126 17380_AT 2127 17394_S_AT 20640_S_AT 2128 17398_AT 2129 17448_AT 2130 17485_S_AT 2131 17490_S_AT 2132 17499_S_AT 2133 17505_S_AT 2134 17516_S_AT 2135 17529_S_AT 2136 17543_S_AT 2137 17593_R_AT 19858_S_AT 2138 17609_AT 2139 17698_AT 2140 17836_AT 2141 17886_AT 2142 17896_AT 2143 17901_AT 2144 17902_S_AT 2145 17913_S_AT 2146 17924_AT 2147 17954_S_AT 2148 17960_AT 2149 17991_G_AT 18967_S_AT 2150 17999_AT 2151 18057_I_AT 2152 18078_AT 2153 18091_AT 2154 18168_S_AT 2155 18252_AT 2156 18267_AT 2157 18300_AT 2158 18308_I_AT 2159 18328_AT 2160 18354_AT 2161 18402_AT 2162 18416_AT 2163 18455_AT 2164 18459_AT 2165 18571_AT 2166 18604_AT 19181_S_AT 2167 18644_AT 2168 18745_F_AT 19611_S_AT 2169 18782_AT 2170 18881_AT 2171 18904_S_AT 2172 18914_S_AT 2173 18963_AT 2174 19068_I_AT 2175 19078_AT 2176 19171_AT 2177 19177_AT 2178 19394_AT 2179 19411_AT 2180 19415_AT 2181 19466_S_AT 2182 19484_S_AT 2183 19549_S_AT 2184 19592_AT 2185 19633_AT 2186 19641_AT 2187 19669_AT 2188 19672_AT 2189 19684_AT 2190 19692_AT 2191 19746_AT 2192 19835_AT 2193 19848_S_AT 2194 19892_AT 2195 19904_AT 2196 19936_AT 2197 19974_S_AT 2198 19994_AT 2199 20005_S_AT 2200 20022_AT 2201 20032_AT 2202 20044_AT 2203 20049_AT 2204 20081_AT 2205 20133_I_AT 2206 20155_S_AT 2207 20163_S_AT 2208 20200_AT 2209 20296_S_AT 2210 20336_AT 2211 20341_AT 2212 20372_AT 2213 20385_S_AT 2214 20433_AT 2215 20489_AT 2216 20525_AT 2217 20543_AT 2218 20565_AT 2219 20570_AT 2220 20576_AT 2221 20577_AT 2222 20609_AT 2223 20646_AT 2224 20672_AT 2225 20707_S_AT 2226 20720_AT

TABLE 19 2X UP IN SALT & COLD, ONLY 12004_at 12098_at 12148_at 12251_at 12357_s_at 12394_at 12457_at 12505_s_at 12522_at 12541_at 12594_at 12606_at 12697_at 12745_at 12781_at 12798_at 12855_f_at 12945_at 12951_at 13005_at 13015_s_at 13115_at 13146_s_at 13335_at 13447_s_at 13480_at 13544_at 13549_at 13580_at 13649_at 13943_at 13950_s_at 14110_i_at 14144_at 14224_at 14432_at 14468_at 14479_at 14524_s_at 14640_s_at 14643_s_at 14735_s_at 14737_s_at 14768_at 14784_at 14924_at 15064_at 15127_s_at 15186_s_at 15189_s_at 15255_at 15389_at 15482_at 15495_at 15496_at 15519_s_at 15580_s_at 15582_s_at 15776_at 15798_at 15910_at 15931_at 15937_at 15949_s_at 15972_s_at 16048_at 16086_s_at 16120_s_at 16126_s_at 16150_s_at 16159_s_at 16230_at 16306_at 16418_s_at 16423_at 16449_s_at 16565_s_at 16603_s_at 16763_at 16968_at 16983_at 17002_at 17015_s_at 17019_s_at 17078_s_at 17232_at 17317_at 17394_s_at 17516_s_at 17585_s_at 17609_at 17698_at 17836_at 17896_at 17899_at 17902_s_at 17960_at 17963_at 18168_s_at 18252_at 18267_at 18308_i_at 18354_at 18402_at 18459_at 18484_at 18745_f_at 18904_s_at 18914_s_at 18929_s_at 18946_at 18963_at 19078_at 19137_at 19141_at 19411_at 19641_at 19672_at 19684_at 19692_at 19746_at 19762_at 19869_at 19894_at 19904_at 19936_at 19994_at 20005_s_at 20031_at 20044_at 20382_s_at 20406_g_at 20421_at 20525_at 20543_at 20565_at 20570_at 20640_s_at 20646_at 20720_at

TABLE 20 2X DOWN IN COLD & SALT, ONLY 12021_at 12094_at 12128_at 12151_at 12332_s_at 12472_s_at 12475_at 12482_s_at 12490_at 12531_at 12540_s_at 12577_at 12629_at 12642_at 12660_at 12676_s_at 12712_f_at 12725_r_at 12777_i_at 12790_s_at 12801_at 12887_s_at 12933_r_at 13153_r_at 13228_at 13362_s_at 13428_at 13538_at 13565_at 13588_at 13696_at 13702_s_at 13716_at 13764_at 14050_at 14055_s_at 14069_at 14078_at 14232_at 14346_at 14608_at 14609_at 14621_at 14635_s_at 14663_s_at 14688_s_at 14691_at 14704_s_at 14875_at 14911_s_at 14964_at 15022_at 15085_s_at 15123_s_at 15153_s_at 15172_s_at 15190_s_at 15211_s_at 15241_s_at 15437_at 15562_at 15638_s_at 15647_s_at 15654_s_at 15655_s_at 15658_s_at 15695_s_at 15846_at 15930_at 16053_i_at 16078_s_at 16229_at 16465_at 16484_s_at 16596_s_at 16600_s_at 16642_s_at 16914_s_at 17027_s_at 17066_s_at 17083_s_at 17128_s_at 17380_at 17398_at 17448_at 17485_s_at 17490_s_at 17499_s_at 17505_s_at 17514_s_at 17593_r_at 17886_at 17913_s_at 17924_at 17954_s_at 17991_g_at 18057_i_at 18069_at 18328_at 18416_at 18604_at 18644_at 18881_at 19171_at 19181_s_at 19182_at 19394_at 19415_at 19466_s_at 19549_s_at 19592_at 19633_at 19669_at 19848_s_at 19858_s_at 19878_at 19892_at 19974_s_at 20022_at 20032_at 20049_at 20081_at 20155_s_at 20163_s_at 20296_s_at 20336_at 20341_at 20365_s_at 20372_at 20489_at 20491_at 20576_at 20577_at 20609_at 20672_at

TABLE 21 OSMOTIC & SALINE STRESS RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 2586 12126_S_AT 2587 12137_AT 2588 12227_AT 2589 12239_AT 2590 12268_AT 2591 12369_AT 2592 12476_AT 2593 12484_G_AT 2594 12494_AT 2595 12644_AT 2596 12645_AT 2597 12796_S_AT 2598 12819_AT 2599 12841_AT 2600 12852_S_AT 19455_S_AT 2601 13084_AT 2602 13171_AT 2603 13174_R_AT 2604 13596_AT 2605 13807_AT 2606 13977_AT 2607 13999_AT 2608 14052_AT 2609 14293_AT 2610 14335_AT 2611 14486_AT 2612 14506_AT 2613 14518_AT 2614 14540_AT 2615 14578_S_AT 2616 14646_S_AT 2617 14662_F_AT 15962_S_AT 2618 14901_AT 2619 14918_AT 2620 14986_AT 2621 15053_S_AT 2622 15179_S_AT 2623 15252_G_AT 2624 15280_AT 2625 15467_AT 2626 15607_S_AT 2627 15625_S_AT 2628 15703_I_AT 2629 15827_AT 2630 15863_AT 2631 15923_AT 2632 15946_S_AT 2633 16005_S_AT 2634 16073_F_AT 2635 16114_S_AT 2636 16127_S_AT 18744_F_AT 2637 16190_AT 2638 16196_AT 2639 16236_G_AT 19531_AT 2640 16310_AT 2641 16316_AT 2642 16334_S_AT 2643 16335_AT 2644 16340_AT 2645 16450_S_AT 2646 16500_AT 2647 16524_AT 2648 16533_AT 2649 16690_G_AT 2650 16762_AT 2651 16819_AT 2652 16873_I_AT 2653 16972_AT 2654 16991_AT 2655 17099_S_AT 2656 17339_AT 2657 17397_S_AT 2658 17419_AT 2659 17460_AT 2660 17554_S_AT 2661 17939_AT 2662 18013_R_AT 18178_S_AT 2663 18024_S_AT 2664 18032_I_AT 2665 18054_AT 2666 18151_AT 2667 18281_AT 2668 18445_AT 2669 18520_AT 2670 18583_AT 2671 18663_S_AT 2672 18753_S_AT 2673 18876_AT 2674 18938_G_AT 2675 18971_AT 2676 18977_AT 2677 18981_AT 2678 19099_AT 2679 19196_AT 2680 19376_AT 2681 19409_AT 2682 19503_AT 2683 19826_AT 2684 19847_S_AT 2685 19930_AT 2686 19992_AT 2687 20096_AT 2688 20108_AT 2689 20256_S_AT 2690 20290_S_AT 2691 20298_AT 2692 20305_AT 2693 20322_AT 2694 20333_AT 2695 20402_S_AT 2696 20424_AT 2697 20446_S_AT 2698 20450_AT 2699 20468_AT 2700 20569_S_AT 2701 20639_AT 2702 20678_AT 2703 20686_AT

TABLE 22 2X UP IN SALT & MANNITOL, ONLY 12126_s_at 12227_at 12369_at 12521_at 12644_at 12645_at 12724_f_at 12795_at 12796_s_at 12841_at 12852_s_at 12958_at 13014_at 13174_r_at 13211_s_at 13596_at 13640_at 13789_at 13977_at 13999_at 14069_at 14083_at 14089_at 14293_at 14675_s_at 15053_s_at 15058_s_at 15252_g_at 15280_at 15437_at 15607_s_at 15625_s_at 15827_at 15863_at 15880_at 16005_s_at 16031_at 16073_f_at 16316_at 16334_s_at 16335_at 16450_s_at 16500_at 16524_at 16533_at 16597_s_at 16819_at 17085_s_at 17099_s_at 17339_at 17419_at 17442_i_at 17514_s_at 17548_s_at 17554_s_at 17961_at 18032_i_at 18054_at 18151_at 18167_s_at 18281_at 18520_at 18663_s_at 18744_f_at 18753_s_at 18789_at 18876_at 18909_s_at 18938_g_at 18977_at 19099_at 19108_at 19135_at 19227_at 19376_at 19429_at 19455_s_at 19531_at 19789_s_at 19878_at 20017_at 20096_at 20256_s_at 20290_s_at 20305_at 20322_at 20333_at 20420_at 20424_at 20689_s_at

TABLE 23 2X DOWN IN MANNITOL & SALT, ONLY 12239_at 12251_at 12476_at 12484_g_at 12494_at 12561_at 12647_s_at 12719_f_at 12819_at 12841_at 13084_at 13171_at 13172_s_at 13435_at 13807_at 14250_r_at 14335_at 14486_at 14506_at 14518_at 14901_at 15046_s_at 15179_s_at 15451_at 15703_i_at 15946_s_at 16014_s_at 16114_s_at 16310_at 16342_at 16712_at 16762_at 16972_at 16991_at 17397_s_at 17408_at 17460_at 17775_at 17939_at 18445_at 18583_at 18751_f_at 18971_at 18981_at 19156_s_at 19196_at 19359_s_at 19409_at 19503_at 19713_at 19718_at 19847_s_at 19930_at 20108_at 20298_at 20421_at 20432_at 20446_s_at 20639_at

TABLE 24 COLD, OSMOTIC & SALINE RESPONSIVE SEQUENCES AFFYMETRIX SEQ ID NO: ID NO: 1262 12004_AT 1263 12023_S_AT 1264 12078_AT 1265 12115_AT 1266 12118_AT 1267 12150_AT 1268 12251_AT 1269 12271_S_AT 1270 12276_AT 1271 12332_S_AT 13211_S_AT 1272 12338_AT 1273 12400_AT 1274 12430_AT 1275 12457_AT 1276 12521_AT 1277 12522_AT 1278 12530_AT 1279 12536_S_AT 1280 12538_AT 1281 12561_AT 1282 12574_AT 19019_I_AT 1283 12595_AT 1284 12606_AT 1285 12609_AT 1286 12622_AT 1287 12630_AT 1288 12647_S_AT 1289 12676_S_AT 1290 12697_AT 1291 12698_AT 1292 12719_F_AT 1293 12724_F_AT 15871_S_AT 16597_S_AT 1294 12749_AT 1295 12765_AT 1296 12769_AT 1297 12781_AT 1298 12785_AT 1299 12792_S_AT 1300 12795_AT 1301 12805_S_AT 1302 12857_AT 1303 12883_S_AT 1304 12909_S_AT 16539_S_AT 1305 12932_S_AT 15605_S_AT 1306 12945_AT 1307 12958_AT 1308 12964_AT 1309 12968_AT 1310 12972_AT 1311 12989_S_AT 1312 13004_AT 1313 13014_AT 1314 13025_AT 1315 13036_AT 1316 13099_S_AT 1317 13136_AT 1318 13146_S_AT 13239_S_AT 1319 13153_R_AT 1320 13159_AT 1321 13176_AT 1322 13217_S_AT 17500_S_AT 1323 13225_S_AT 15997_S_AT 1324 13230_S_AT 15972_S_AT 1325 13279_S_AT 17477_S_AT 1326 13280_S_AT 20301_S_AT 1327 13282_S_AT 17027_S_AT 1328 13426_AT 1329 13432_AT 1330 13435_AT 1331 13447_S_AT 1332 13474_AT 1333 13511_AT 1334 13546_AT 1335 13547_S_AT 1336 13548_AT 1337 13555_AT 1338 13587_AT 1339 13595_AT 1340 13610_S_AT 1341 13627_AT 1342 13640_AT 1343 13645_AT 1344 13647_AT 1345 13706_S_AT 19701_S_AT 1346 13716_AT 18228_AT 1347 13725_AT 1348 13764_AT 1349 13771_AT 1350 13789_AT 1351 13916_AT 1352 13965_S_AT 1353 13967_AT 1354 14028_AT 1355 14039_AT 1356 14046_AT 1357 14049_AT 1358 14069_AT 1359 14077_AT 1360 14080_AT 1361 14083_AT 1362 14089_AT 1363 14090_I_AT 1364 14097_AT 1365 14116_AT 1366 14151_AT 14219_AT 1367 14170_AT 1368 14172_AT 1369 14192_AT 1370 14224_AT 1371 14227_AT 1372 14244_S_AT 14245_AT 14645_S_AT 15974_G_AT 1373 14248_AT 1374 14250_R_AT 1375 14367_AT 1376 14381_AT 1377 14384_AT 1378 14398_S_AT 1379 14487_AT 1380 14582_AT 1381 14597_AT 1382 14609_AT 1383 14612_AT 19267_S_AT 1384 14614_AT 1385 14636_S_AT 1386 14644_S_AT 14658_S_AT 14659_S_AT 15964_S_AT 1387 14675_S_AT 1388 14691_AT 14709_AT 1389 14704_S_AT 15846_AT 1390 14705_I_AT 1391 14733_S_AT 1392 14735_S_AT 1393 14779_AT 1394 14784_AT 1395 14923_AT 1396 14947_AT 1397 14950_AT 1398 14990_AT 1399 14998_AT 1400 15005_S_AT 1401 15018_AT 1402 15045_AT 1403 15046_S_AT 1404 15052_AT 1405 15058_S_AT 1406 15064_AT 1407 15088_S_AT 1408 15098_S_AT 1409 15103_S_AT 1410 15109_S_AT 1411 15124_S_AT 1412 15127_S_AT 1413 15145_S_AT 1414 15154_S_AT 1415 15161_S_AT 1416 15189_S_AT 1417 15214_S_AT 1418 15255_AT 1419 15356_AT 1420 15357_AT 1421 15364_AT 1422 15392_AT 1423 15403_S_AT 1424 15437_AT 1425 15451_AT 1426 15476_AT 1427 15482_AT 1428 15483_S_AT 1429 15521_S_AT 1430 15522_I_AT 1431 15531_I_AT 1432 15573_AT 1433 15581_S_AT 1434 15586_S_AT 1435 15594_S_AT 1436 15609_S_AT 1437 15611_S_AT 1438 15621_F_AT 1439 15623_F_AT 1440 15669_S_AT 1441 15695_S_AT 1442 15702_S_AT 1443 15753_AT 1444 15761_AT 1445 15776_AT 1446 15778_AT 1447 15839_AT 1448 15842_AT 1449 15857_S_AT 1450 15859_AT 1451 15880_AT 1452 15886_AT 1453 15906_S_AT 1454 15910_AT 1455 15937_AT 1456 15957_AT 1457 15970_S_AT 1458 15985_AT 1459 16010_S_AT 16011_S_AT 17078_S_AT 1460 16021_S_AT 1461 16031_AT 1462 16038_S_AT 1463 16045_S_AT 1464 16046_S_AT 1465 16048_AT 1466 16061_S_AT 1467 16082_S_AT 1468 16111_F_AT 1469 16115_S_AT 1470 16141_S_AT 1471 16144_S_AT 1472 16163_S_AT 1473 16173_S_AT 1474 16229_AT 1475 16298_AT 1476 16301_S_AT 1477 16322_AT 1478 16342_AT 1479 16351_AT 1480 16412_S_AT 1481 16422_AT 1482 16427_AT 1483 16438_AT 1484 16474_S_AT 1485 16482_S_AT 1486 16485_S_AT 18052_S_AT 1487 16493_AT 1488 16534_S_AT 1489 16555_S_AT 1490 16561_S_AT 17572_S_AT 1491 16592_S_AT 1492 16615_S_AT 1493 16637_S_AT 1494 16692_AT 1495 16712_AT 1496 16789_AT 1497 16818_S_AT 1498 16971_S_AT 1499 17018_S_AT 1500 17019_S_AT 1501 17029_S_AT 1502 17041_S_AT 1503 17047_S_AT 1504 17066_S_AT 1505 17085_S_AT 1506 17089_S_AT 1507 17179_AT 1508 17180_AT 1509 17228_AT 1510 17252_AT 1511 17317_AT 1512 17338_AT 1513 17384_AT 1514 17387_S_AT 1515 17400_S_AT 1516 17407_S_AT 1517 17408_AT 1518 17413_S_AT 1519 17416_AT 1520 17425_S_AT 1521 17440_I_AT 1522 17442_I_AT 1523 17473_AT 1524 17484_AT 1525 17514_S_AT 1526 17520_S_AT 1527 17533_S_AT 1528 17548_S_AT 19614_AT 1529 17549_S_AT 1530 17555_S_AT 1531 17567_AT 1532 17654_AT 1533 17693_AT 1534 17697_AT 1535 17722_AT 1536 17752_AT 1537 17755_AT 1538 17775_AT 1539 17832_S_AT 1540 17840_S_AT 1541 17843_S_AT 1542 17855_AT 1543 17860_AT 1544 17869_AT 1545 17888_AT 1546 17899_AT 1547 17929_S_AT 1548 17930_S_AT 1549 17932_S_AT 1550 17936_S_AT 18670_G_AT 1551 17957_AT 1552 17961_AT 1553 17962_AT 1554 17963_AT 1555 17971_S_AT 1556 17975_AT 18742_F_AT 1557 18016_R_AT 1558 18069_AT 1559 18122_AT 1560 18140_AT 1561 18199_AT 1562 18224_S_AT 1563 18225_AT 1564 18235_AT 1565 18259_S_AT 1566 18265_AT 1567 18270_AT 1568 18280_AT 1569 18289_AT 1570 18296_AT 1571 18298_AT 1572 18314_I_AT 1573 18318_AT 1574 18325_AT 1575 18351_S_AT 1576 18471_AT 1577 18482_S_AT 1578 18484_AT 1579 18560_AT 1580 18564_AT 1581 18590_AT 1582 18594_AT 1583 18595_AT 1584 18596_AT 1585 18629_S_AT 1586 18637_AT 1587 18661_AT 1588 18668_AT 1589 18699_I_AT 1590 18747_F_AT 18789_AT 1591 18761_AT 1592 18833_AT 1593 18875_S_AT 1594 18894_AT 1595 18936_AT 1596 18946_AT 1597 18953_AT 1598 18955_AT 1599 18972_AT 1600 19008_S_AT 1601 19108_AT 1602 19123_AT 1603 19135_AT 1604 19137_AT 1605 19141_AT 1606 19152_AT 1607 19156_S_AT 1608 19182_AT 1609 19186_S_AT 1610 19214_AT 1611 19216_AT 1612 19227_AT 1613 19243_AT 1614 19288_AT 1615 19359_S_AT 1616 19368_AT 1617 19379_AT 1618 19380_S_AT 1619 19398_AT 1620 19421_AT 1621 19424_AT 1622 19429_AT 1623 19430_AT 1624 19450_AT 1625 19457_AT 1626 19467_AT 1627 19516_AT 1628 19545_AT 1629 19564_AT 1630 19577_AT 1631 19593_AT 1632 19602_AT 1633 19618_AT 1634 19638_AT 1635 19640_AT 1636 19646_S_AT 1637 19656_S_AT 1638 19670_AT 1639 19696_AT 1640 19713_AT 1641 19718_AT 1642 19722_S_AT 1643 19749_AT 1644 19755_AT 1645 19762_AT 1646 19789_S_AT 1647 19815_AT 1648 19843_AT 1649 19869_AT 1650 19878_AT 1651 19883_AT 1652 19894_AT 1653 19926_AT 1654 19944_AT 1655 19968_AT 1656 19977_AT 1657 19982_AT 1658 19987_AT 1659 19991_AT 1660 20015_AT 1661 20017_AT 1662 20031_AT 1663 20040_AT 1664 20042_S_AT 1665 20060_AT 20438_AT 1666 20089_AT 1667 20118_AT 1668 20144_AT 1669 20149_AT 1670 20179_AT 1671 20190_AT 1672 20194_AT 1673 20219_AT 1674 20245_S_AT 1675 20263_AT 1676 20308_S_AT 1677 20335_S_AT 1678 20338_AT 1679 20345_AT 1680 20365_S_AT 1681 20382_S_AT 1682 20390_S_AT 1683 20395_AT 1684 20420_AT 1685 20421_AT 1686 20432_AT 1687 20437_AT 1688 20442_I_AT 1689 20463_S_AT 1690 20491_AT 1691 20537_AT 1692 20573_AT 1693 20636_AT 1694 20638_AT 1695 20641_AT 1696 20658_S_AT 1697 20689_S_AT 1698 20698_S_AT

TABLE 25 2X UP IN COLD, SALT & MANNITOL 12023_s_at 12332_s_at 12530_at 12536_s_at 12574_at 12595_at 12698_at 12749_at 12765_at 12769_at 12785_at 12857_at 12964_at 12972_at 12989_s_at 13004_at 13025_at 13036_at 13099_s_at 13136_at 13176_at 13220_s_at 13225_s_at 13230_s_at 13239_s_at 13426_at 13474_at 13548_at 13555_at 13595_at 13627_at 13645_at 13647_at 13706_s_at 13965_s_at 13967_at 14080_at 14090_i_at 14097_at 14116_at 14151_at 14172_at 14192_at 14244_s_at 14245_at 14367_at 14398_s_at 14582_at 14614_at 14644_s_at 14645_s_at 14658_s_at 14659_s_at 14733_s_at 14923_at 14990_at 15005_s_at 15018_at 15052_at 15088_s_at 15098_s_at 15103_s_at 15145_s_at 15154_s_at 15161_s_at 15214_s_at 15356_at 15521_s_at 15573_at 15586_s_at 15609_s_at 15611_s_at 15621_f_at 15669_s_at 15695_s_at 15753_at 15761_at 15857_s_at 15871_s_at 15964_s_at 15970_s_at 15974_g_at 15997_s_at 16011_s_at 16021_s_at 16038_s_at 16046_s_at 16082_s_at 16111_f_at 16115_s_at 16127_s_at 16141_s_at 16144_s_at 16163_s_at 16236_g_at 16301_s_at 16322_at 16422_at 16474_s_at 16482_s_at 16485_s_at 16555_s_at 16561_s_at 16592_s_at 16637_s_at 17041_s_at 17047_s_at 17179_at 17180_at 17252_at 17384_at 17407_s_at 17484_at 17520_s_at 17555_s_at 17572_s_at 17722_at 17752_at 17840_s_at 17843_s_at 17860_at 17929_s_at 17936_s_at 17962_at 18052_s_at 18069_at 18122_at 18199_at 18259_s_at 18280_at 18289_at 18314_i_at 18318_at 18325_at 18482_s_at 18590_at 18594_at 18595_at 18596_at 18629_s_at 18661_at 18668_at 18699_i_at 18722_s_at 18936_at 18953_at 18955_at 18972_at 19008_s_at 19152_at 19186_s_at 19214_at 19368_at 19379_at 19380_s_at 19421_at 19545_at 19614_at 19638_at 19640_at 19646_s_at 19656_s_at 19701_s_at 19843_at 19944_at 19982_at 19987_at 19991_at 20042_s_at 20060_at 20118_at 20144_at 20149_at 20179_at 20194_at 20245_s_at 20390_s_at 20437_at 20463_s_at 20491_at 20641_at 20658_s_at

TABLE 26 2X DOWN IN COLD, MANNITOL & SALT, ONLY 12078_at 12115_at 12118_at 12150_at 12271_s_at 12276_at 12338_at 12400_at 12430_at 12538_at 12622_at 12630_at 12792_s_at 12805_s_at 12883_s_at 12909_s_at 12932_s_at 12968_at 13159_at 13217_s_at 13279_s_at 13282_s_at 13432_at 13511_at 13546_at 13547_s_at 13587_at 13610_s_at 13640_at 13725_at 13771_at 13916_at 14028_at 14039_at 14046_at 14049_at 14077_at 14170_at 14227_at 14248_at 14381_at 14384_at 14487_at 14597_at 14705_i_at 14709_at 14779_at 14947_at 14950_at 14998_at 15045_at 15109_s_at 15124_s_at 15189_s_at 15357_at 15364_at 15403_s_at 15476_at 15483_s_at 15522_i_at 15531_i_at 15594_s_at 15702_s_at 15778_at 15839_at 15842_at 15859_at 15872_at 15880_at 15886_at 15906_s_at 15957_at 15985_at 16045_s_at 16061_s_at 16173_s_at 16298_at 16351_at 16412_s_at 16438_at 16493_at 16534_s_at 16539_s_at 16615_s_at 16692_at 16789_at 16818_s_at 16971_s_at 17018_s_at 17029_s_at 17089_s_at 17228_at 17338_at 17387_s_at 17413_s_at 17416_at 17425_s_at 17440_i_at 17473_at 17533_s_at 17549_s_at 17654_at 17693_at 17697_at 17755_at 17832_s_at 17869_at 17888_at 17930_s_at 17932_s_at 17957_at 17963_at 17971_s_at 17975_at 18016_r_at 18140_at 18224_s_at 18225_at 18228_at 18235_at 18265_at 18270_at 18296_at 18298_at 18471_at 18564_at 18637_at 18742_f_at 18761_at 18833_at 18875_s_at 18894_at 18946_at 19123_at 19216_at 19243_at 19267_s_at 19288_at 19398_at 19424_at 19430_at 19450_at 19457_at 19467_at 19516_at 19564_at 19577_at 19593_at 19602_at 19618_at 19670_at 19696_at 19722_s_at 19749_at 19755_at 19815_at 19926_at 19968_at 19977_at 20015_at 20040_at 20089_at 20190_at 20219_at 20263_at 20301_s_at 20308_s_at 20338_at 20345_at 20395_at 20442_i_at 20537_at 20573_at 20636_at 20638_at 20698_s_at

TABLE 27 2X ROOT SPECIFIC (COLD, SALINE & OSMOTIC STRESSES) 11997_at 12004_at 12051_at 12072_at 12150_at 12151_at 12166_i_at 12219_at 12315_at 12332_s_at 12374_i_at 12482_s_at 12515_at 12522_at 12538_at 12571_s_at 12574_at 12609_at 12678_i_at 12698_at 12749_at 12760_g_at 12765_at 12768_at 12769_at 12772_at 12777_i_at 12958_at 12989_s_at 13015_s_at 13134_s_at 13146_s_at 13172_s_at 13178_at 13179_at 13187_i_at 13211_s_at 13239_s_at 13273_s_at 13297_s_at 13549_at 13604_at 13629_s_at 13706_s_at 13714_at 13751_at 13895_at 13933_at 13967_at 13985_s_at 14028_at 14030_at 14058_at 14069_at 14072_at 14073_at 14097_at 14139_at 14235_at 14250_r_at 14578_s_at 14582_at 14640_s_at 14643_s_at 14644_s_at 14658_s_at 14659_s_at 14711_s_at 14900_at 14924_at 14990_at 15018_at 15022_at 15107_s_at 15116_f_at 15120_s_at 15124_s_at 15131_s_at 15132_s_at 15137_s_at 15184_s_at 15188_s_at 15208_s_at 15252_g_at 15343_at 15389_at 15392_at 15448_at 15503_at 15531_i_at 15594_s_at 15609_s_at 15623_f_at 15639_s_at 15670_s_at 15680_s_at 15859_at 15900_at 15923_at 15962_s_at 15964_s_at 15965_at 15975_s_at 15985_at 16001_at 16048_at 16052_at 16053_i_at 16105_s_at 16161_s_at 16165_s_at 16298_at 16334_s_at 16422_at 16427_at 16440_s_at 16442_s_at 16468_at 16488_at 16511_at 16529_at 16553_f_at 16568_s_at 16914_s_at 16965_s_at 16981_s_at 16989_at 17033_s_at 17066_s_at 17085_s_at 17252_at 17376_at 17378_at 17388_at 17415_at 17429_s_at 17463_at 17485_s_at 17490_s_at 17567_at 17585_s_at 17595_s_at 17840_s_at 17860_at 17880_s_at 17894_at 17896_at 17899_at 17911_at 17935_at 17961_at 18024_s_at 18122_at 18222_at 18224_s_at 18252_at 18255_at 18269_s_at 18270_at 18327_s_at 18597_at 18607_s_at 18636_at 18663_s_at 18782_at 18885_at 18888_at 18942_at 18955_at 19060_at 19108_at 19135_at 19137_at 19195_at 19263_at 19376_at 19406_at 19432_s_at 19835_at 19836_at 19840_s_at 19841_at 19843_at 19926_at 19972_at 19977_at 19991_at 20034_i_at 20042_s_at 20189_at 20194_at 20200_at 20214_i_at 20239_g_at 20262_at 20269_at 20294_at 20312_s_at 20382_s_at 20396_at 20432_at 20444_at 20446_s_at 20480_s_at 20586_i_at 20612_s_at 20672_at 20686_at 20689_s_at

TABLE 28 2X LEAF SPECIFIC (COLD, SALINE & OSMOTIC STRESSES) 12169_i_at 12186_at 12187_at 12211_at 12212_at 12214_g_at 12270_at 12645_at 12754_g_at 12774_at 12793_at 12796_s_at 12910_s_at 12916_s_at 12953_at 13090_at 13124_at 13335_at 13550_at 13567_at 13568_at 13596_at 13614_at 13678_s_at 13719_at 14014_at 14096_at 14118_i_at 14369_at 14478_at 14513_s_at 14540_at 14596_at 14733_s_at 14986_at 15045_at 15097_s_at 15098_s_at 15145_s_at 15153_s_at 15154_s_at 15182_s_at 15203_s_at 15372_at 15521_s_at 15581_s_at 15621_f_at 15642_s_at 15776_at 15910_at 16017_at 16046_s_at 16115_s_at 16136_s_at 16172_s_at 16316_at 16385_s_at 16455_at 16485_s_at 16512_s_at 16547_s_at 16548_s_at 16629_s_at 16673_at 16899_at 17010_s_at 17018_s_at 17054_s_at 17095_s_at 17097_s_at 17273_at 17394_s_at 17420_at 17449_s_at 17600_s_at 17843_s_at 17913_s_at 17966_at 18003_at 18081_at 18560_at 18588_at 18626_at 18644_at 18666_s_at 18742_f_at 18977_at 18994_at 19227_at 19373_at 19834_at 19867_at 19998_at 20062_at 20199_at 20256_s_at 20284_at 20437_at 20442_i_at 20450_at 20468_at 20547_at 20635_s_at

TABLE 29 2X TRANSCRIPTION (COLD, SALINE & OSMOTIC STRESSES) 12068_at 12166_i_at 12374_i_at 12392_at 12431_at 12450_s_at 12503_at 12536_s_at 12540_s_at 12541_at 12587_at 12594_at 12595_at 12704_f_at 12705_f_at 12709_f_at 12712_f_at 12719_f_at 12724_f_at 12725_r_at 12726_f_at 12734_f_at 12736_f_at 12737_f_at 12812_at 12949_at 12951_at 12966_s_at 13023_at 13034_s_at 13087_at 13270_at 13273_s_at 13432_at 13555_at 13688_s_at 13714_at 13965_s_at 13987_s_at 14003_at 14144_at 14178_at 14223_at 14235_at 14303_s_at 14393_at 14553_at 14781_at 15046_s_at 15053_s_at 15214_s_at 15510_r_at 15638_s_at 15665_s_at 15679_s_at 15720_at 15871_s_at 16072_s_at 16073_f_at 16105_s_at 16111_f_at 16127_s_at 16534_s_at 16582_s_at 16589_s_at 16747_at 17019_s_at 17129_s_at 17160_at 17520_s_at 17538_s_at 17555_s_at 17609_at 17896_at 17971_s_at 17975_at 17978_s_at 18121_s_at 18167_s_at 18197_at 18222_at 18318_at 18576_s_at 18629_s_at 18738_f_at 18742_f_at 18744_f_at 18745_f_at 18747_f_at 18750_f_at 18751_f_at 18789_at 18834_at 18942_at 19083_at 19202_at 19209_s_at 19232_s_at 19315_at 19489_s_at 19611_s_at 19646_s_at 19707_s_at 19722_s_at 19744_at 19755_at 19836_at 19860_at 19866_at 19898_at 20262_at 20335_s_at 20362_at 20424_at 20437_at 20456_at 20515_s_at 20635_s_at

TABLE 30 2X PHOSPHATES (COLD, SALINE & OSMOTIC STRESSES) 12470_at 12556_at 13128_at 13135_s_at 13180_s_at 13192_s_at 13193_s_at 13587_at 13995_at 14335_at 15073_at 15171_s_at 15240_at 15586_s_at 15641_s_at 15651_f_at 15990_at 16232_s_at 16576_f_at 16753_at 17423_s_at 17525_s_at 17537_s_at 17929_s_at 17954_s_at 18012_s_at 18308_i_at 18616_at 18847_at 18936_at 18980_at 19243_at 19263_at 19638_at 19883_at 19932_at 20333_at 20393_at 20570_at

TABLE 31 2X KINASES (COLD, SALINE & OSMOTIC STRESSES) 12253_g_at 12270_at 12271_s_at 12276_at 12278_at 12284_at 12300_at 12307_at 12353_at 12357_s_at 12390_at 12394_at 12395_s_at 12408_at 12452_at 12477_at 12490_at 12497_at 12532_at 12697_at 12901_s_at 12902_at 12958_at 12959_at 13068_at 13246_at 13324_at 13332_at 13362_s_at 13370_at 13550_at 14030_at 14048_at 14194_at 14196_at 14217_at 14459_at 14603_at 14637_s_at 14686_s_at 15005_s_at 15175_s_at 15270_at 15475_s_at 15497_s_at 15577_s_at 15616_s_at 15633_s_at 15634_s_at 15668_s_at 15680_s_at 15798_at 16034_at 16059_s_at 16087_s_at 16088_f_at 16125_s_at 16137_s_at 16140_s_at 16143_s_at 16144_s_at 16160_f_at 16171_s_at 16357_at 16412_s_at 16568_s_at 16570_s_at 16571_s_at 16584_s_at 16651_s_at 16652_s_at 16672_at 16818_s_at 16840_at 17068_s_at 17122_s_at 17252_at 17323_at 17475_at 17752_at 17921_s_at 17933_at 17935_at 18013_r_at 18046_s_at 18122_at 18176_at 18316_at 18455_at 18459_at 18482_s_at 18543_at 18706_s_at 18782_at 18924_at 19117_s_at 19437_s_at 19442_at 19458_at 19464_at 19469_at 19562_at 19655_at 19749_at 19854_at 19904_at 20144_at 20219_at 20223_at 20232_s_at 20235_i_at 20282_s_at 20298_at 20396_at 20439_at 20462_at 

1. A transgenic plant, which contains a transgene comprising a polynucleotide derived from a plant stress-regulated gene.
 2. The transgenic plant of claim 1, wherein the transgene comprises a nucleotide sequence having at least 90% sequence identity to a nucleotide sequence set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
 3. The transgenic plant of claim 1, wherein the polynucleotide is a regulatory element a plant stress-regulated gene, and has a sequence set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379
 4. The transgenic plant of claim 3, wherein the polynucleotide has sequence is set forth in SEQ ID NO:3780.
 5. The transgenic plant of claim 1, wherein the transgene comprises a plant stress-regulated regulatory element operatively linked to a heterologous nucleotide sequence.
 6. The transgenic plant of claim 5, wherein the transgenic plant expresses a polypeptide encoded by the heterologous nucleotide sequence.
 7. The transgenic plant of claim 6, wherein the polypeptide improves the nutritional value or ornamental value of the plant.
 8. The transgenic plant of claim 1, wherein the transgene comprises a coding sequence of a plant stress-regulated gene, and has a nucleotide sequence set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, and 1929-2703.
 9. The transgenic plant of claim 1, wherein the transgenic plant exhibits altered responsiveness to a stress condition as compared to a corresponding wild-type plant.
 10. The transgenic plant of claim 1, wherein the transgene disrupts an endogenous stress-regulated gene in the plant, thereby reducing or inhibiting expression of the gene in response to a stress condition.
 11. The transgenic plant of claim 1, wherein the plant exhibits increased tolerance to a stress condition.
 12. The transgenic plant of claim 1, wherein the plant exhibits decreased tolerance to a stress condition.
 13. A regulatory element of a plant stress-regulated gene which has at least 90% sequence identity to a nucleotide sequence as set forth in any of 2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
 14. The regulatory element of claim 13, comprising a nucleotide sequence as set forth in SEQ ID NO:3780.
 15. A method of expressing a heterologous nucleotide sequence in a plant cell, the method comprising introducing into the plant cell a regulatory element of claim 13 operatively linked to the heterologous nucleotide sequence, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell.
 16. The method of claim 15, wherein the heterologous nucleotide sequence encodes a selectable marker.
 17. The method of claim 15, wherein the heterologous nucleotide sequence encodes a polypeptide that improves the nutritional value or the ornamental value of the plant cell.
 18. A method of identifying an agent that modulates the activity of a regulatory element of a plant stress-regulated gene, the method comprising: a) contacting a regulatory element of a plant stress-regulated gene of claim 13 with an agent suspected of having the ability to modulate the activity of the regulatory element; and b) detecting a change in the activity of the regulatory element, thereby identifying an agent that modulates the activity of the plant stress-regulated regulatory element.
 19. The method of claim 18, wherein the regulatory element is operatively linked to a heterologous nucleotide sequence.
 20. The method of claim 19, wherein the heterologous nucleotide sequence encodes a reporter molecule. 